rs2965101

Variant names:

• chr19-44734556-T-C
• rs2965101

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.345 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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.351

Alfa AF: 0.339 Hom.: 18393

Bravo AF: 0.347

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2965101; hg19: chr19-45237812;