rs6661074

Variant names:

• chr1-205369991-G-A
• rs6661074

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.402 in 152,080 control chromosomes in the GnomAD database, including 13,352 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 0.40 (13352 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61171 AN: 151962 Hom.: 13343 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.402 AC: 61201 AN: 152080 Hom.: 13352 Cov.: 33 AF XY: 0.409 AC XY: 30392 AN XY: 74342

African (AFR) AF: 0.225 AC: 9337 AN: 41484

American (AMR) AF: 0.513 AC: 7842 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2295 AN: 5176

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4820

European-Finnish (FIN) AF: 0.535 AC: 5636 AN: 10544

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31388 AN: 67986

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.446 Hom.: 66596

Bravo AF: 0.397

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	18
DANN	Benign	0.71
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6661074; hg19: chr1-205339119;