rs4901972

Variant names:

• chr14-60220695-C-A
• rs4901972

Your query was ambiguous. Multiple possible variants found:

• chr14-60220695-C-A
• chr14-60220695-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 0.012 in 152,268 control chromosomes in the GnomAD database, including 43 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 0.012 (43 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0793 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: 0.0119 AC: 1816 AN: 152150 Hom.: 43 Cov.: 31

Gnomad AFR AF: 0.00261

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.00747

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00223

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0120 AC: 1822 AN: 152268 Hom.: 43 Cov.: 31 AF XY: 0.0140 AC XY: 1044 AN XY: 74444

Gnomad4 AFR AF: 0.00260

Gnomad4 AMR AF: 0.0490

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.0858

Gnomad4 SAS AF: 0.00747

Gnomad4 FIN AF: 0.0257

Gnomad4 NFE AF: 0.00223

Gnomad4 OTH AF: 0.0165

Alfa AF: 0.00678 Hom.: 4

Bravo AF: 0.0149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4901972; hg19: chr14-60687413;