rs1408580

Variant names:

• chr10-100100874-C-T
• rs1408580
• ENST00000807894.1:n.430+4637C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000807894.1(ENSG00000305032):​n.430+4637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000305032 ENST00000807894.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 1 publications found

Genes affected

ENSG00000305032 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807894.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305032	ENST00000807894.1		n.430+4637C>T		intron	N/A

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

African (AFR) AF: 0.102 AC: 4251 AN: 41528

American (AMR) AF: 0.0476 AC: 727 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.0626 AC: 324 AN: 5178

South Asian (SAS) AF: 0.0410 AC: 198 AN: 4828

European-Finnish (FIN) AF: 0.104 AC: 1103 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0654 AC: 4448 AN: 67994

Other (OTH) AF: 0.0747 AC: 158 AN: 2116

Alfa AF: 0.0638 Hom.: 593

Bravo AF: 0.0732

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.51
PhyloP100		-0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1408580;

hg19: chr10-101860631;