chr9-79167270-A-G

Variant names:

• chr9-79167270-A-G
• rs1361536
• ENST00000650036.1:n.403+15916T>C

Variant summary

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

The ENST00000650036.1(ENSG00000260995):​n.403+15916T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,966 control chromosomes in the GnomAD database, including 35,374 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 (35374 hom., cov: 31)
• Consequence: ENSG00000260995 ENST00000650036.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 5 publications found

Genes affected

ENSG00000260995 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 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
ENSG00000260995	ENST00000650036.1	n.403+15916T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.678 AC: 103022 AN: 151848 Hom.: 35360 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.678 AC: 103075 AN: 151966 Hom.: 35374 Cov.: 31 AF XY: 0.677 AC XY: 50313 AN XY: 74268

African (AFR) AF: 0.750 AC: 31112 AN: 41464

American (AMR) AF: 0.746 AC: 11385 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2538 AN: 3464

East Asian (EAS) AF: 0.763 AC: 3934 AN: 5158

South Asian (SAS) AF: 0.565 AC: 2719 AN: 4810

European-Finnish (FIN) AF: 0.617 AC: 6504 AN: 10544

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42567 AN: 67958

Other (OTH) AF: 0.712 AC: 1503 AN: 2112

Alfa AF: 0.648 Hom.: 128492

Bravo AF: 0.694

Asia WGS AF: 0.639 AC: 2222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1361536; hg19: chr9-81782185;