17-79849763-G-T

Variant names:

• chr17-79849763-G-T
• rs1622986
• ENST00000570408.1:n.213+135C>A

Variant summary

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

The ENST00000570408.1(ENSG00000262343):​n.213+135C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,108 control chromosomes in the GnomAD database, including 14,689 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 0.42 (14689 hom., cov: 33)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: ENSG00000262343 ENST00000570408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 4 publications found

Genes affected

ENSG00000262343 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262343	ENST00000570408.1	n.213+135C>A		intron_variant	Intron 1 of 1	2
ENSG00000262343	ENST00000719653.1	n.73-1595C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63460 AN: 151980 Hom.: 14684 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.417 AC: 63480 AN: 152098 Hom.: 14689 Cov.: 33 AF XY: 0.417 AC XY: 30982 AN XY: 74352

African (AFR) AF: 0.234 AC: 9729 AN: 41492

American (AMR) AF: 0.449 AC: 6866 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1751 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5166

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4818

European-Finnish (FIN) AF: 0.583 AC: 6161 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 35045 AN: 67986

Other (OTH) AF: 0.430 AC: 906 AN: 2106

Alfa AF: 0.461 Hom.: 8017

Bravo AF: 0.401

Asia WGS AF: 0.199 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.032
DANN	Benign	0.42
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1622986; hg19: chr17-77823562;