rs7662743

Variant names:

• chr4-46174811-G-A
• rs7662743

Variant summary

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

The variant allele was found at a frequency of 0.433 in 151,830 control chromosomes in the GnomAD database, including 14,676 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 (14676 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65755 AN: 151712 Hom.: 14665 Cov.: 31

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.433 AC: 65809 AN: 151830 Hom.: 14676 Cov.: 31 AF XY: 0.429 AC XY: 31860 AN XY: 74192

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.424

Alfa AF: 0.463 Hom.: 7738

Bravo AF: 0.429

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7662743; hg19: chr4-46176828;