rs7262634

Variant names:

• chr20-47205635-T-C
• rs7262634
• ENST00000746722.1:n.144-2987T>C

Variant summary

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

The ENST00000746722.1(ENSG00000297275):​n.144-2987T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0864 in 152,250 control chromosomes in the GnomAD database, including 727 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 0.086 (727 hom., cov: 32)
• Consequence: ENSG00000297275 ENST00000746722.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 6 publications found

Genes affected

ENSG00000297275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746722.1. 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
	ENSG00000297275	ENST00000746722.1		n.144-2987T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0864 AC: 13140 AN: 152132 Hom.: 724 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0930

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

GnomAD4 genome AF: 0.0864 AC: 13160 AN: 152250 Hom.: 727 Cov.: 32 AF XY: 0.0887 AC XY: 6602 AN XY: 74460

African (AFR) AF: 0.144 AC: 5963 AN: 41534

American (AMR) AF: 0.0740 AC: 1132 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3472

East Asian (EAS) AF: 0.0505 AC: 262 AN: 5190

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4816

European-Finnish (FIN) AF: 0.0505 AC: 536 AN: 10604

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0513 AC: 3486 AN: 68018

Other (OTH) AF: 0.0944 AC: 199 AN: 2108

Alfa AF: 0.0644 Hom.: 1808

Bravo AF: 0.0894

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.89
DANN	Benign	0.39
PhyloP100		-0.97

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: rs7262634;

hg19: chr20-45834279;