rs2044061

Variant names:

• chr8-19865992-T-C
• rs2044061

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 0.317 in 152,026 control chromosomes in the GnomAD database, including 8,057 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 0.32 (8057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.317 AC: 48217 AN: 151908 Hom.: 8046 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.317 AC: 48237 AN: 152026 Hom.: 8057 Cov.: 32 AF XY: 0.321 AC XY: 23886 AN XY: 74318

African (AFR) AF: 0.247 AC: 10251 AN: 41478

American (AMR) AF: 0.369 AC: 5642 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2468 AN: 5156

South Asian (SAS) AF: 0.425 AC: 2045 AN: 4812

European-Finnish (FIN) AF: 0.398 AC: 4209 AN: 10568

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

European-Non Finnish (NFE) AF: 0.321 AC: 21830 AN: 67956

Other (OTH) AF: 0.304 AC: 641 AN: 2106

Alfa AF: 0.317 Hom.: 32456

Bravo AF: 0.313

Asia WGS AF: 0.478 AC: 1656 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.73
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs2044061; hg19: chr8-19723503;