rs7656846

Variant names:

• chr4-107455184-C-A
• rs7656846

Your query was ambiguous. Multiple possible variants found:

• chr4-107455184-C-A
• chr4-107455184-C-G
• chr4-107455184-C-T

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 0.751 in 152,088 control chromosomes in the GnomAD database, including 43,233 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 0.75 (43233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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: 0.751 AC: 114096 AN: 151970 Hom.: 43183 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.751 AC: 114205 AN: 152088 Hom.: 43233 Cov.: 32 AF XY: 0.751 AC XY: 55826 AN XY: 74316

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.743

Alfa AF: 0.724 Hom.: 5012

Bravo AF: 0.755

Asia WGS AF: 0.828 AC: 2877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7656846; hg19: chr4-108376341;