rs1408580

Positions:

• chr10-100100874-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 0.0754 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;