chr6-31194377-G-A

Variant names:

• chr6-31194377-G-A
• rs28362332
• ENST00000755443.1:n.182+3397C>T

Variant summary

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

The ENST00000755443.1(ENSG00000272501):​n.182+3397C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,210 control chromosomes in the GnomAD database, including 1,236 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 0.12 (1236 hom., cov: 33)
• Consequence: ENSG00000272501 ENST00000755443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 15 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 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.182+3397C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18609 AN: 152092 Hom.: 1234 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.122 AC: 18632 AN: 152210 Hom.: 1236 Cov.: 33 AF XY: 0.127 AC XY: 9416 AN XY: 74420

African (AFR) AF: 0.104 AC: 4308 AN: 41534

American (AMR) AF: 0.155 AC: 2377 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3468

East Asian (EAS) AF: 0.108 AC: 561 AN: 5178

South Asian (SAS) AF: 0.141 AC: 679 AN: 4826

European-Finnish (FIN) AF: 0.185 AC: 1960 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7561 AN: 68012

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.122 Hom.: 1117

Bravo AF: 0.122

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		1.4

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: rs28362332;

hg19: chr6-31162154;