3-164526631-T-C

Variant names:

• chr3-164526631-T-C
• rs967422
• ENST00000701346.1:n.258+75096T>C

Variant summary

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

The ENST00000701346.1(ENSG00000289884):​n.258+75096T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,114 control chromosomes in the GnomAD database, including 999 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 0.11 (999 hom., cov: 32)
• Consequence: ENSG00000289884 ENST00000701346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 6 publications found

Genes affected

ENSG00000289884 (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 (AMR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701346.1. 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
	ENSG00000289884	ENST00000701346.1		n.258+75096T>C		intron	N/A
	ENSG00000289884	ENST00000702159.2		n.302+75096T>C		intron	N/A
	ENSG00000289884	ENST00000721983.1		n.84+75874T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16184 AN: 151996 Hom.: 996 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.106 AC: 16196 AN: 152114 Hom.: 999 Cov.: 32 AF XY: 0.107 AC XY: 7969 AN XY: 74360

African (AFR) AF: 0.0727 AC: 3022 AN: 41542

American (AMR) AF: 0.150 AC: 2287 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3466

East Asian (EAS) AF: 0.0366 AC: 189 AN: 5166

South Asian (SAS) AF: 0.100 AC: 483 AN: 4826

European-Finnish (FIN) AF: 0.141 AC: 1493 AN: 10598

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8094 AN: 67936

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.110 Hom.: 1399

Bravo AF: 0.106

Asia WGS AF: 0.0530 AC: 184 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	6.6
DANN	Benign	0.78
PhyloP100		-0.19

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: rs967422;

hg19: chr3-164244419;