rs410644

Variant names:

• chr5-81791715-G-T
• rs410644
• ENST00000781613.1:n.250+22489C>A

Variant summary

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

The ENST00000781613.1(ENSG00000301766):​n.250+22489C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,034 control chromosomes in the GnomAD database, including 31,719 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 0.64 (31719 hom., cov: 32)
• Consequence: ENSG00000301766 ENST00000781613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 9 publications found

Genes affected

ENSG00000301766 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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
ENSG00000301766	ENST00000781613.1	n.250+22489C>A		intron_variant	Intron 2 of 2
ENSG00000301766	ENST00000781614.1	n.462-22052C>A		intron_variant	Intron 3 of 3
ENSG00000301766	ENST00000781615.1	n.351-22052C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96586 AN: 151916 Hom.: 31659 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.636 AC: 96702 AN: 152034 Hom.: 31719 Cov.: 32 AF XY: 0.633 AC XY: 47013 AN XY: 74314

African (AFR) AF: 0.806 AC: 33442 AN: 41490

American (AMR) AF: 0.667 AC: 10193 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1852 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3323 AN: 5170

South Asian (SAS) AF: 0.519 AC: 2500 AN: 4818

European-Finnish (FIN) AF: 0.568 AC: 5987 AN: 10546

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37466 AN: 67946

Other (OTH) AF: 0.604 AC: 1278 AN: 2116

Alfa AF: 0.578 Hom.: 88519

Bravo AF: 0.657

Asia WGS AF: 0.550 AC: 1910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.24
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs410644; hg19: chr5-81087534;