rs162201

Variant names:

• chr9-99318136-A-G
• rs162201
• ENST00000726034.1:n.610-419A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-99318136-A-G
• chr9-99318136-A-T

Variant summary

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

The ENST00000726034.1(ENSG00000294793):​n.610-419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,106 control chromosomes in the GnomAD database, including 20,221 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 0.51 (20221 hom., cov: 32)
• Consequence: ENSG00000294793 ENST00000726034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 6 publications found

Genes affected

ENSG00000294793 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726034.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294793	ENST00000726034.1		n.610-419A>G		intron	N/A
	ENSG00000294793	ENST00000726035.1		n.1338-419A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77891 AN: 151988 Hom.: 20213 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.512 AC: 77929 AN: 152106 Hom.: 20221 Cov.: 32 AF XY: 0.515 AC XY: 38280 AN XY: 74372

African (AFR) AF: 0.477 AC: 19796 AN: 41474

American (AMR) AF: 0.558 AC: 8541 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3828 AN: 5170

South Asian (SAS) AF: 0.495 AC: 2387 AN: 4824

European-Finnish (FIN) AF: 0.531 AC: 5616 AN: 10572

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33964 AN: 67984

Other (OTH) AF: 0.547 AC: 1155 AN: 2112

Alfa AF: 0.506 Hom.: 5216

Bravo AF: 0.513

Asia WGS AF: 0.653 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.64

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs162201;

hg19: chr9-102080418;

COSMIC: COSV60381385;