chr17-57788926-G-A

Variant names:

• chr17-57788926-G-A
• rs12938916
• ENST00000580960.2:n.264-16730C>T

Variant summary

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

The ENST00000580960.2(ENSG00000265542):​n.264-16730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,220 control chromosomes in the GnomAD database, including 282 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 0.055 (282 hom., cov: 32)
• Consequence: ENSG00000265542 ENST00000580960.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 11 publications found

Genes affected

ENSG00000265542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580960.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000265542	ENST00000580960.2	TSL:2	n.264-16730C>T		intron	N/A
	ENSG00000265542	ENST00000581805.5	TSL:2	n.222-16730C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8301 AN: 152102 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0478

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0547 AC: 8319 AN: 152220 Hom.: 282 Cov.: 32 AF XY: 0.0566 AC XY: 4216 AN XY: 74426

African (AFR) AF: 0.0490 AC: 2036 AN: 41538

American (AMR) AF: 0.0536 AC: 819 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.0318 AC: 165 AN: 5190

South Asian (SAS) AF: 0.161 AC: 778 AN: 4824

European-Finnish (FIN) AF: 0.0537 AC: 568 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0523 AC: 3559 AN: 68006

Other (OTH) AF: 0.0487 AC: 103 AN: 2114

Alfa AF: 0.0542 Hom.: 690

Bravo AF: 0.0515

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.4
DANN	Benign	0.76
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12938916;

hg19: chr17-55866287;