rs10418380

Variant names:

• chr19-7659654-A-G
• rs10418380

Your query was ambiguous. Multiple possible variants found:

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

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 0.315 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.311 AC: 12867 AN: 41436

American (AMR) AF: 0.294 AC: 4482 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5168

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4816

European-Finnish (FIN) AF: 0.355 AC: 3741 AN: 10552

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21777 AN: 67968

Other (OTH) AF: 0.310 AC: 652 AN: 2106

Alfa AF: 0.316 Hom.: 31383

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
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10418380; hg19: chr19-7724540;