19-7674291-T-C

Variant names:

• chr19-7674291-T-C
• rs1423096

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 0.914 in 152,158 control chromosomes in the GnomAD database, including 63,662 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 0.91 (63662 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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 = 0.945 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: 0.914 AC: 138961 AN: 152040 Hom.: 63611 Cov.: 31

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.914 AC: 139072 AN: 152158 Hom.: 63662 Cov.: 31 AF XY: 0.913 AC XY: 67877 AN XY: 74370

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.924

Alfa AF: 0.907 Hom.: 46322

Bravo AF: 0.918

Asia WGS AF: 0.877 AC: 3052 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	1.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1423096; hg19: chr19-7739177;