rs9263846

Variant names:

• chr6-31187893-G-A
• rs9263846
• ENST00000755443.1:n.183-1623C>T

Variant summary

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

The ENST00000755443.1(ENSG00000272501):​n.183-1623C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,976 control chromosomes in the GnomAD database, including 2,309 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 0.16 (2309 hom., cov: 31)
• Consequence: ENSG00000272501 ENST00000755443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 13 publications found

Genes affected

ENSG00000272501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755443.1. 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
	ENSG00000272501	ENST00000755443.1		n.183-1623C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24950 AN: 151858 Hom.: 2308 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.164 AC: 24970 AN: 151976 Hom.: 2309 Cov.: 31 AF XY: 0.170 AC XY: 12602 AN XY: 74268

African (AFR) AF: 0.119 AC: 4940 AN: 41468

American (AMR) AF: 0.213 AC: 3254 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1332 AN: 3464

East Asian (EAS) AF: 0.122 AC: 631 AN: 5168

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2374 AN: 10550

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10611 AN: 67934

Other (OTH) AF: 0.228 AC: 479 AN: 2102

Alfa AF: 0.175 Hom.: 2464

Bravo AF: 0.164

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.36
PhyloP100		0.22

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: rs9263846;

hg19: chr6-31155670;