rs61835656

Variant names:

• chr1-226796726-A-T
• rs61835656

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 0.281 in 151,926 control chromosomes in the GnomAD database, including 7,426 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 0.28 (7426 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42747 AN: 151810 Hom.: 7423 Cov.: 31

Gnomad AFR AF: 0.0795

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.281 AC: 42737 AN: 151926 Hom.: 7426 Cov.: 31 AF XY: 0.280 AC XY: 20789 AN XY: 74268

African (AFR) AF: 0.0793 AC: 3287 AN: 41432

American (AMR) AF: 0.285 AC: 4347 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1143 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5168

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4818

European-Finnish (FIN) AF: 0.367 AC: 3867 AN: 10524

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26425 AN: 67930

Other (OTH) AF: 0.300 AC: 632 AN: 2104

Alfa AF: 0.334 Hom.: 1189

Bravo AF: 0.261

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.39
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs61835656; hg19: chr1-226984427; COSMIC: COSV69337779;