rs1160267

Variant names:

• chr8-23672008-G-A
• rs1160267
• ENST00000835200.1:n.475+3258G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-23672008-G-A
• chr8-23672008-G-C
• chr8-23672008-G-T

Variant summary

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

The ENST00000835200.1(ENSG00000308589):​n.475+3258G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,036 control chromosomes in the GnomAD database, including 19,299 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 0.49 (19299 hom., cov: 32)
• Consequence: ENSG00000308589 ENST00000835200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 19 publications found

Genes affected

ENSG00000308589 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986930	XR_001745842.2	n.1312+3258G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308589	ENST00000835200.1	n.475+3258G>A		intron_variant	Intron 4 of 4
ENSG00000308589	ENST00000835201.1	n.1097+3258G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73755 AN: 151918 Hom.: 19296 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.485 AC: 73776 AN: 152036 Hom.: 19299 Cov.: 32 AF XY: 0.486 AC XY: 36076 AN XY: 74304

African (AFR) AF: 0.287 AC: 11882 AN: 41458

American (AMR) AF: 0.525 AC: 8026 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3646 AN: 5166

South Asian (SAS) AF: 0.562 AC: 2711 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5199 AN: 10548

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38626 AN: 67974

Other (OTH) AF: 0.495 AC: 1039 AN: 2100

Alfa AF: 0.538 Hom.: 9092

Bravo AF: 0.481

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1160267; hg19: chr8-23529521;