rs764917

Variant names:

• chr5-111064809-C-A
• rs764917
• ENST00000743602.1:n.29+1626G>T

Variant summary

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

The ENST00000743602.1(ENSG00000296915):​n.29+1626G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,020 control chromosomes in the GnomAD database, including 30,202 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 0.60 (30202 hom., cov: 33)
• Consequence: ENSG00000296915 ENST00000743602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 7 publications found

Genes affected

ENSG00000296915 (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 (AFR) allele frequency at 95% confidence interval = 0.869 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
ENSG00000296915	ENST00000743602.1	n.29+1626G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91641 AN: 151902 Hom.: 30150 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.604 AC: 91750 AN: 152020 Hom.: 30202 Cov.: 33 AF XY: 0.602 AC XY: 44687 AN XY: 74286

African (AFR) AF: 0.876 AC: 36381 AN: 41510

American (AMR) AF: 0.588 AC: 8979 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1675 AN: 3466

East Asian (EAS) AF: 0.742 AC: 3832 AN: 5164

South Asian (SAS) AF: 0.572 AC: 2757 AN: 4816

European-Finnish (FIN) AF: 0.410 AC: 4320 AN: 10534

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31822 AN: 67938

Other (OTH) AF: 0.598 AC: 1264 AN: 2112

Alfa AF: 0.512 Hom.: 33055

Bravo AF: 0.629

Asia WGS AF: 0.681 AC: 2367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.38
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs764917; hg19: chr5-110400507;