rs4927680

Variant names:

• chr3-195932298-A-G
• rs4927680
• ENST00000607976.2:n.611+16944T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641484.1(ENSG00000290762):​n.1500-8088T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,000 control chromosomes in the GnomAD database, including 9,552 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 0.35 (9552 hom., cov: 32)
• Consequence: ENSG00000290762 ENST00000641484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

ENSG00000290762 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 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
ENSG00000290762	ENST00000607976.2	n.611+16944T>C		intron_variant	Intron 2 of 2	6
ENSG00000290762	ENST00000641484.1	n.1500-8088T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53486 AN: 151882 Hom.: 9536 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.352 AC: 53535 AN: 152000 Hom.: 9552 Cov.: 32 AF XY: 0.352 AC XY: 26119 AN XY: 74296

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.374

Alfa AF: 0.365 Hom.: 1251

Bravo AF: 0.346

Asia WGS AF: 0.280 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4927680; hg19: chr3-195659169;