17-44176643-C-G

Variant names:

• chr17-44176643-C-G
• rs7220138
• NM_080863.5:c.570-95C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080863.5(ASB16):​c.570-95C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 1,578,052 control chromosomes in the GnomAD database, including 99,835 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (15798 hom., cov: 32)
  • Exomes 𝑓: 0.33 (84037 hom.)
• Consequence: ASB16 NM_080863.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 26 publications found

Genes affected

ASB16 (HGNC:19768): (ankyrin repeat and SOCS box containing 16) The protein encoded by this gene is a member of the ankyrin repeat and SOCS box-containing (ASB) family of proteins. They contain ankyrin repeat sequence and a SOCS box domain. The SOCS box serves to couple suppressor of cytokine signalling (SOCS) proteins and their binding partners with the elongin B and C complex, possibly targeting them for degradation. [provided by RefSeq, Jul 2008]

ASB16-AS1 (HGNC:25442): (ASB16 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASB16	NM_080863.5	c.570-95C>G		intron_variant	Intron 2 of 4	ENST00000293414.6	NP_543139.4
ASB16-AS1	NR_049729.1	n.1589G>C		non_coding_transcript_exon_variant	Exon 4 of 4
ASB16-AS1	NR_049730.1	n.252-1G>C		splice_acceptor_variant, intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASB16	ENST00000293414.6	c.570-95C>G		intron_variant	Intron 2 of 4	1	NM_080863.5	ENSP00000293414.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65079 AN: 151866 Hom.: 15758 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.401

GnomAD2 exomes AF: 0.389 AC: 96638 AN: 248656 AF XY: 0.371

Gnomad AFR exome AF: 0.643

Gnomad AMR exome AF: 0.445

Gnomad ASJ exome AF: 0.482

Gnomad EAS exome AF: 0.785

Gnomad FIN exome AF: 0.322

Gnomad NFE exome AF: 0.302

Gnomad OTH exome AF: 0.367

GnomAD4 exome AF: 0.329 AC: 468673 AN: 1426068 Hom.: 84037 Cov.: 27 AF XY: 0.326 AC XY: 231962 AN XY: 711504

African (AFR) AF: 0.643 AC: 21021 AN: 32670

American (AMR) AF: 0.445 AC: 19855 AN: 44632

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 12431 AN: 25854

East Asian (EAS) AF: 0.742 AC: 29278 AN: 39456

South Asian (SAS) AF: 0.290 AC: 24592 AN: 84750

European-Finnish (FIN) AF: 0.319 AC: 17039 AN: 53344

Middle Eastern (MID) AF: 0.339 AC: 1934 AN: 5702

European-Non Finnish (NFE) AF: 0.297 AC: 320392 AN: 1080496

Other (OTH) AF: 0.374 AC: 22131 AN: 59164

GnomAD4 genome AF: 0.429 AC: 65180 AN: 151984 Hom.: 15798 Cov.: 32 AF XY: 0.429 AC XY: 31897 AN XY: 74298

African (AFR) AF: 0.634 AC: 26275 AN: 41452

American (AMR) AF: 0.434 AC: 6622 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1684 AN: 3466

East Asian (EAS) AF: 0.773 AC: 3984 AN: 5154

South Asian (SAS) AF: 0.306 AC: 1477 AN: 4824

European-Finnish (FIN) AF: 0.315 AC: 3331 AN: 10576

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20601 AN: 67942

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.283 Hom.: 1094

Bravo AF: 0.454

Asia WGS AF: 0.521 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7220138; hg19: chr17-42254011; COSMIC: COSV53234804; COSMIC: COSV53234804;