rs34124816

Positions:

• chr19-7668790-A-C

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 0.0518 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.00518

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0411

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0475

Alfa AF: 0.0499 Hom.: 26

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34124816; hg19: chr19-7733676;