rs4122017

chr6-147984816-T-C

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 0.441 in 152,066 control chromosomes in the GnomAD database, including 16,377 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 0.44 (16377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67080 AN: 151948 Hom.: 16371 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.441 AC: 67104 AN: 152066 Hom.: 16377 Cov.: 32 AF XY: 0.445 AC XY: 33113 AN XY: 74338

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.465

Alfa AF: 0.500 Hom.: 19929

Bravo AF: 0.421

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.9
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4122017; hg19: chr6-148305952; COSMIC: COSV60290667;