chr19-29878103-T-G

Variant names:

• chr19-29878103-T-G
• rs34724

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 0.502 in 151,406 control chromosomes in the GnomAD database, including 19,547 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 0.50 (19547 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 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: 0.502 AC: 75985 AN: 151288 Hom.: 19540 Cov.: 28

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.502 AC: 76009 AN: 151406 Hom.: 19547 Cov.: 28 AF XY: 0.501 AC XY: 37048 AN XY: 73910

African (AFR) AF: 0.381 AC: 15704 AN: 41260

American (AMR) AF: 0.517 AC: 7853 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3468

East Asian (EAS) AF: 0.514 AC: 2615 AN: 5086

South Asian (SAS) AF: 0.506 AC: 2396 AN: 4732

European-Finnish (FIN) AF: 0.495 AC: 5190 AN: 10482

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38159 AN: 67860

Other (OTH) AF: 0.529 AC: 1119 AN: 2114

Alfa AF: 0.540 Hom.: 61186

Bravo AF: 0.497

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.11
DANN	Benign	0.35
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs34724; hg19: chr19-30369010;