rs6666757

Variant names:

• chr1-26576203-A-T
• rs6666757

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 0.153 in 152,138 control chromosomes in the GnomAD database, including 2,176 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 0.15 (2176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.980
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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: 0.153 AC: 23326 AN: 152020 Hom.: 2176 Cov.: 32

Gnomad AFR AF: 0.0599

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.153 AC: 23328 AN: 152138 Hom.: 2176 Cov.: 32 AF XY: 0.153 AC XY: 11406 AN XY: 74370

African (AFR) AF: 0.0598 AC: 2483 AN: 41534

American (AMR) AF: 0.106 AC: 1616 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3468

East Asian (EAS) AF: 0.142 AC: 730 AN: 5156

South Asian (SAS) AF: 0.154 AC: 742 AN: 4818

European-Finnish (FIN) AF: 0.226 AC: 2387 AN: 10578

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14150 AN: 67976

Other (OTH) AF: 0.155 AC: 327 AN: 2112

Alfa AF: 0.189 Hom.: 385

Bravo AF: 0.139

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.54
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs6666757; hg19: chr1-26902694; COSMIC: COSV65175732;