19-32490396-T-G

Variant names:

• chr19-32490396-T-G
• rs7245958

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 0.178 in 152,168 control chromosomes in the GnomAD database, including 3,277 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 0.18 (3277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 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: 0.178 AC: 27036 AN: 152050 Hom.: 3255 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0973

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.178 AC: 27093 AN: 152168 Hom.: 3277 Cov.: 32 AF XY: 0.182 AC XY: 13520 AN XY: 74402

African (AFR) AF: 0.300 AC: 12429 AN: 41480

American (AMR) AF: 0.148 AC: 2264 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2328 AN: 5164

South Asian (SAS) AF: 0.267 AC: 1288 AN: 4826

European-Finnish (FIN) AF: 0.119 AC: 1265 AN: 10598

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6622 AN: 68010

Other (OTH) AF: 0.167 AC: 353 AN: 2116

Alfa AF: 0.123 Hom.: 723

Bravo AF: 0.183

Asia WGS AF: 0.390 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs7245958; hg19: chr19-32981302;