rs6510725

Variant names:

• chr19-348743-T-C
• rs6510725

Your query was ambiguous. Multiple possible variants found:

• chr19-348743-T-C
• chr19-348743-T-G

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 0.518 in 151,916 control chromosomes in the GnomAD database, including 21,082 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 0.52 (21082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 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: 0.519 AC: 78712 AN: 151798 Hom.: 21087 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.518 AC: 78730 AN: 151916 Hom.: 21082 Cov.: 32 AF XY: 0.520 AC XY: 38589 AN XY: 74224

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.514

Alfa AF: 0.519 Hom.: 7881

Bravo AF: 0.514

Asia WGS AF: 0.663 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6510725; hg19: chr19-348743;