rs71365421

Variant names:

• chr19-54037413-G-A
• rs71365421

Your query was ambiguous. Multiple possible variants found:

• chr19-54037413-G-A
• chr19-54037413-G-T

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 0.211 in 151,438 control chromosomes in the GnomAD database, including 3,617 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 0.21 (3617 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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: 0.211 AC: 31859 AN: 151320 Hom.: 3617 Cov.: 29

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.211 AC: 31879 AN: 151438 Hom.: 3617 Cov.: 29 AF XY: 0.215 AC XY: 15914 AN XY: 73956

African (AFR) AF: 0.151 AC: 6220 AN: 41326

American (AMR) AF: 0.318 AC: 4800 AN: 15078

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3468

East Asian (EAS) AF: 0.356 AC: 1830 AN: 5134

South Asian (SAS) AF: 0.287 AC: 1373 AN: 4786

European-Finnish (FIN) AF: 0.214 AC: 2245 AN: 10478

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13745 AN: 67868

Other (OTH) AF: 0.222 AC: 466 AN: 2098

Alfa AF: 0.0923 Hom.: 122

Bravo AF: 0.216

Asia WGS AF: 0.315 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.62
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs71365421; hg19: chr19-54540667; COSMIC: COSV58076167;