rs10414410

Variant names:

• chr19-29595100-C-A
• rs10414410

Your query was ambiguous. Multiple possible variants found:

• chr19-29595100-C-A
• chr19-29595100-C-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 0.428 in 152,032 control chromosomes in the GnomAD database, including 14,149 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 0.43 (14149 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 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: 0.428 AC: 65016 AN: 151912 Hom.: 14140 Cov.: 33

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.428 AC: 65060 AN: 152032 Hom.: 14149 Cov.: 33 AF XY: 0.430 AC XY: 31935 AN XY: 74324

African (AFR) AF: 0.408 AC: 16929 AN: 41450

American (AMR) AF: 0.489 AC: 7480 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1830 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2668 AN: 5170

South Asian (SAS) AF: 0.362 AC: 1743 AN: 4818

European-Finnish (FIN) AF: 0.420 AC: 4428 AN: 10554

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28600 AN: 67978

Other (OTH) AF: 0.462 AC: 975 AN: 2110

Alfa AF: 0.423 Hom.: 14164

Bravo AF: 0.437

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.29
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10414410; hg19: chr19-30086007;