chr7-19287465-C-T

Variant names:

• chr7-19287465-C-T
• rs2191892

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 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

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;