rs731956

Variant names:

• chr8-83952066-A-G
• rs731956
• ENST00000523678.1:n.123+39231A>G

Variant summary

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

The ENST00000523678.1(ENSG00000254202):​n.123+39231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,988 control chromosomes in the GnomAD database, including 3,076 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 0.17 (3076 hom., cov: 32)
• Consequence: ENSG00000254202 ENST00000523678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 3 publications found

Genes affected

ENSG00000254202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523678.1. 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
	ENSG00000254202	ENST00000523678.1	TSL:3	n.123+39231A>G		intron	N/A
	ENSG00000254202	ENST00000752019.1		n.142-2257A>G		intron	N/A
	ENSG00000254202	ENST00000752020.1		n.142-12014A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25698 AN: 151868 Hom.: 3063 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.170 AC: 25762 AN: 151988 Hom.: 3076 Cov.: 32 AF XY: 0.167 AC XY: 12399 AN XY: 74302

African (AFR) AF: 0.340 AC: 14081 AN: 41436

American (AMR) AF: 0.115 AC: 1754 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3466

East Asian (EAS) AF: 0.150 AC: 773 AN: 5156

South Asian (SAS) AF: 0.174 AC: 837 AN: 4818

European-Finnish (FIN) AF: 0.0744 AC: 790 AN: 10622

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6989 AN: 67932

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.121 Hom.: 6224

Bravo AF: 0.178

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.090
DANN	Benign	0.37
PhyloP100		-2.4

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: rs731956;

hg19: chr8-84864301;