rs61783628

Variant names:

• chr1-28882595-C-T
• rs61783628

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 0.274 in 152,178 control chromosomes in the GnomAD database, including 6,864 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 0.27 (6864 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 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: 0.274 AC: 41648 AN: 152060 Hom.: 6860 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.274 AC: 41663 AN: 152178 Hom.: 6864 Cov.: 33 AF XY: 0.281 AC XY: 20879 AN XY: 74384

African (AFR) AF: 0.102 AC: 4224 AN: 41564

American (AMR) AF: 0.318 AC: 4855 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.0700 AC: 362 AN: 5172

South Asian (SAS) AF: 0.290 AC: 1399 AN: 4824

European-Finnish (FIN) AF: 0.436 AC: 4609 AN: 10576

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.358 AC: 24330 AN: 67982

Other (OTH) AF: 0.267 AC: 564 AN: 2114

Alfa AF: 0.296 Hom.: 1122

Bravo AF: 0.253

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs61783628; hg19: chr1-29209107;