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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.462

Alfa AF: 0.420 Hom.: 8467

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10414410; hg19: chr19-30086007;