chr19-44734556-T-C

Variant names:

• chr19-44734556-T-C
• rs2965101

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 0.345 in 151,632 control chromosomes in the GnomAD database, including 9,126 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 0.34 (9126 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 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: 0.345 AC: 52210 AN: 151512 Hom.: 9123 Cov.: 29

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.345 AC: 52238 AN: 151632 Hom.: 9126 Cov.: 29 AF XY: 0.343 AC XY: 25415 AN XY: 74112

African (AFR) AF: 0.389 AC: 16036 AN: 41272

American (AMR) AF: 0.316 AC: 4799 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1630 AN: 5140

South Asian (SAS) AF: 0.478 AC: 2295 AN: 4798

European-Finnish (FIN) AF: 0.269 AC: 2844 AN: 10570

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21839 AN: 67866

Other (OTH) AF: 0.351 AC: 740 AN: 2110

Alfa AF: 0.337 Hom.: 28612

Bravo AF: 0.347

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2965101; hg19: chr19-45237812;