rs4955720

Variant names:

• chr3-170310812-A-C
• rs4955720

Your query was ambiguous. Multiple possible variants found:

• chr3-170310812-A-C
• chr3-170310812-A-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 0.668 in 151,376 control chromosomes in the GnomAD database, including 34,373 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 0.67 (34373 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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: 0.668 AC: 101026 AN: 151276 Hom.: 34323 Cov.: 30

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.668 AC: 101128 AN: 151376 Hom.: 34373 Cov.: 30 AF XY: 0.664 AC XY: 49091 AN XY: 73900

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.671

Alfa AF: 0.634 Hom.: 17176

Bravo AF: 0.682

Asia WGS AF: 0.727 AC: 2530 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.94
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4955720; hg19: chr3-170028600;