rs2191892

Positions:

• chr7-19287465-C-T

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 0.113 in 151,554 control chromosomes in the GnomAD database, including 1,905 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 0.11 (1905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17146 AN: 151436 Hom.: 1904 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0892

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

GnomAD4 genome AF: 0.113 AC: 17164 AN: 151554 Hom.: 1905 Cov.: 31 AF XY: 0.109 AC XY: 8101 AN XY: 74068

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.0620

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.0638 Hom.: 288

Bravo AF: 0.123

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2191892; hg19: chr7-19327088;