rs1965861

Variant names:

• chr6-159461689-A-G
• rs1965861
• ENST00000809869.1:n.75+1520T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-159461689-A-G
• chr6-159461689-A-T

Variant summary

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

The ENST00000809869.1(ENSG00000305262):​n.75+1520T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,976 control chromosomes in the GnomAD database, including 30,370 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 0.63 (30370 hom., cov: 32)
• Consequence: ENSG00000305262 ENST00000809869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 2 publications found

Genes affected

ENSG00000305262 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 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
ENSG00000305262	ENST00000809869.1	n.75+1520T>C		intron_variant	Intron 1 of 2
ENSG00000305262	ENST00000809870.1	n.75+1520T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95241 AN: 151858 Hom.: 30323 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.627 AC: 95346 AN: 151976 Hom.: 30370 Cov.: 32 AF XY: 0.632 AC XY: 46931 AN XY: 74278

African (AFR) AF: 0.512 AC: 21194 AN: 41402

American (AMR) AF: 0.665 AC: 10159 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2117 AN: 3466

East Asian (EAS) AF: 0.708 AC: 3664 AN: 5172

South Asian (SAS) AF: 0.729 AC: 3514 AN: 4822

European-Finnish (FIN) AF: 0.741 AC: 7822 AN: 10554

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44702 AN: 67972

Other (OTH) AF: 0.634 AC: 1340 AN: 2114

Alfa AF: 0.620 Hom.: 3636

Bravo AF: 0.617

Asia WGS AF: 0.703 AC: 2440 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.52
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1965861; hg19: chr6-159882721;