rs6664219

chr1-235547272-G-Achr1-235547272-G-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 0.567 in 151,914 control chromosomes in the GnomAD database, including 25,023 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 0.57 (25023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.567 AC: 86055 AN: 151794 Hom.: 25010 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.567 AC: 86111 AN: 151914 Hom.: 25023 Cov.: 31 AF XY: 0.570 AC XY: 42315 AN XY: 74248

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.597

Alfa AF: 0.575 Hom.: 5412

Bravo AF: 0.567

Asia WGS AF: 0.650 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.6
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6664219; hg19: chr1-235710572; COSMIC: COSV63999086;