rs6668352

Variant names:

• chr1-11854772-G-A
• rs6668352

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.237 in 152,054 control chromosomes in the GnomAD database, including 4,409 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 0.24 (4409 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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: 0.237 AC: 36059 AN: 151934 Hom.: 4415 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.237 AC: 36072 AN: 152054 Hom.: 4409 Cov.: 31 AF XY: 0.236 AC XY: 17504 AN XY: 74310

African (AFR) AF: 0.199 AC: 8269 AN: 41484

American (AMR) AF: 0.182 AC: 2779 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3468

East Asian (EAS) AF: 0.153 AC: 791 AN: 5170

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2676 AN: 10552

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18386 AN: 67972

Other (OTH) AF: 0.253 AC: 533 AN: 2106

Alfa AF: 0.255 Hom.: 6218

Bravo AF: 0.228

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.064
DANN	Benign	0.69
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6668352; hg19: chr1-11914829; COSMIC: COSV64687411;