rs9459971

Variant names:

• chr6-170187139-G-A
• rs9459971
• ENST00000691159.1:n.319-1294C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-170187139-G-A
• chr6-170187139-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000691159.1(ENSG00000230960):​n.319-1294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,568 control chromosomes in the GnomAD database, including 36,588 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 0.68 (36588 hom., cov: 28)
• Consequence: ENSG00000230960 ENST00000691159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

ENSG00000230960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.808 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
ENSG00000230960	ENST00000691159.1	n.319-1294C>T		intron_variant	Intron 1 of 2
ENSG00000230960	ENST00000701993.1	n.275-1294C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.680 AC: 102916 AN: 151450 Hom.: 36558 Cov.: 28

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.679 AC: 102986 AN: 151568 Hom.: 36588 Cov.: 28 AF XY: 0.683 AC XY: 50567 AN XY: 74052

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.694

Alfa AF: 0.751 Hom.: 56077

Bravo AF: 0.661

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9459971; hg19: chr6-170502363;