rs10418380

Positions:

• chr19-7659654-A-G
• chr19-7659654-A-T

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 0.315 in 151,946 control chromosomes in the GnomAD database, including 7,570 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 0.31 (7570 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711

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 = 0.349 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: 0.315 AC: 47802 AN: 151826 Hom.: 7557 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.315 AC: 47855 AN: 151946 Hom.: 7570 Cov.: 31 AF XY: 0.314 AC XY: 23321 AN XY: 74268

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.310

Alfa AF: 0.312 Hom.: 12812

Bravo AF: 0.310

Asia WGS AF: 0.294 AC: 1024 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	3.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10418380; hg19: chr19-7724540;