rs9505192

Variant names:

• chr6-792983-A-G
• rs9505192
• ENST00000658207.1:n.467-3219A>G

Variant summary

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

The ENST00000658207.1(ENSG00000271727):​n.467-3219A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,098 control chromosomes in the GnomAD database, including 18,509 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 0.47 (18509 hom., cov: 33)
• Consequence: ENSG00000271727 ENST00000658207.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 8 publications found

Genes affected

ENSG00000271727 (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 (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658207.1. 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
	ENSG00000271727	ENST00000658207.1		n.467-3219A>G		intron	N/A
	ENSG00000271727	ENST00000669167.1		n.480-3219A>G		intron	N/A
	ENSG00000271727	ENST00000774332.1		n.132-16213A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 71037 AN: 151980 Hom.: 18501 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.467 AC: 71056 AN: 152098 Hom.: 18509 Cov.: 33 AF XY: 0.469 AC XY: 34848 AN XY: 74352

African (AFR) AF: 0.219 AC: 9095 AN: 41500

American (AMR) AF: 0.519 AC: 7927 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3084 AN: 5170

South Asian (SAS) AF: 0.598 AC: 2883 AN: 4818

European-Finnish (FIN) AF: 0.503 AC: 5312 AN: 10554

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39134 AN: 67984

Other (OTH) AF: 0.468 AC: 990 AN: 2114

Alfa AF: 0.528 Hom.: 42934

Bravo AF: 0.457

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.27
PhyloP100		-1.0

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: rs9505192;

hg19: chr6-792983;