rs2191892

Variant names:

• chr7-19287465-C-T
• rs2191892

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 0.113 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.288 AC: 11914 AN: 41310

American (AMR) AF: 0.0580 AC: 880 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3462

East Asian (EAS) AF: 0.0341 AC: 175 AN: 5130

South Asian (SAS) AF: 0.0620 AC: 298 AN: 4806

European-Finnish (FIN) AF: 0.0313 AC: 330 AN: 10556

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3223 AN: 67808

Other (OTH) AF: 0.0892 AC: 187 AN: 2096

Alfa AF: 0.0633 Hom.: 311

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2191892; hg19: chr7-19327088;