rs1408580

Variant names:

• chr10-100100874-C-T
• rs1408580

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 0.0754 in 152,216 control chromosomes in the GnomAD database, including 495 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 0.075 (495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0998 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: 0.0755 AC: 11482 AN: 152098 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0622

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0754 AC: 11484 AN: 152216 Hom.: 495 Cov.: 32 AF XY: 0.0761 AC XY: 5667 AN XY: 74428

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.0410

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0654

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.0631 Hom.: 473

Bravo AF: 0.0732

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408580; hg19: chr10-101860631;