rs2965140

Variant names:

• chr19-44772136-A-G
• rs2965140

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 0.127 in 144,236 control chromosomes in the GnomAD database, including 2,662 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 0.13 (2662 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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: 0.126 AC: 18233 AN: 144142 Hom.: 2635 Cov.: 27

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0397

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.0594

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0846

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.127 AC: 18308 AN: 144236 Hom.: 2662 Cov.: 27 AF XY: 0.127 AC XY: 8799 AN XY: 69414

African (AFR) AF: 0.364 AC: 14315 AN: 39368

American (AMR) AF: 0.0691 AC: 917 AN: 13266

Ashkenazi Jewish (ASJ) AF: 0.0488 AC: 168 AN: 3444

East Asian (EAS) AF: 0.0596 AC: 283 AN: 4752

South Asian (SAS) AF: 0.130 AC: 598 AN: 4596

European-Finnish (FIN) AF: 0.00236 AC: 21 AN: 8890

Middle Eastern (MID) AF: 0.0720 AC: 18 AN: 250

European-Non Finnish (NFE) AF: 0.0261 AC: 1742 AN: 66800

Other (OTH) AF: 0.107 AC: 210 AN: 1964

Alfa AF: 0.0816 Hom.: 209

Bravo AF: 0.137

Asia WGS AF: 0.125 AC: 435 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.088
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2965140; hg19: chr19-45275393;