rs34124816

Variant names:

• chr19-7668790-A-C
• rs34124816

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 0.0518 in 152,054 control chromosomes in the GnomAD database, including 287 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 0.052 (287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0983 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: 0.0518 AC: 7864 AN: 151936 Hom.: 284 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0518 AC: 7881 AN: 152054 Hom.: 287 Cov.: 32 AF XY: 0.0508 AC XY: 3776 AN XY: 74326

African (AFR) AF: 0.0932 AC: 3863 AN: 41450

American (AMR) AF: 0.0364 AC: 557 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00518 AC: 18 AN: 3472

East Asian (EAS) AF: 0.106 AC: 544 AN: 5148

South Asian (SAS) AF: 0.0411 AC: 198 AN: 4822

European-Finnish (FIN) AF: 0.0200 AC: 212 AN: 10574

Middle Eastern (MID) AF: 0.00685 AC: 2 AN: 292

European-Non Finnish (NFE) AF: 0.0350 AC: 2377 AN: 67992

Other (OTH) AF: 0.0475 AC: 100 AN: 2106

Alfa AF: 0.0415 Hom.: 186

Bravo AF: 0.0539

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		-0.29
PromoterAI		-0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs34124816; hg19: chr19-7733676;