rs7661032

Variant names:

• chr4-132985377-T-G
• rs7661032
• ENST00000740310.1:n.246+135A>C

Variant summary

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

The ENST00000740310.1(ENSG00000249513):​n.246+135A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0333 in 152,206 control chromosomes in the GnomAD database, including 195 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 0.033 (195 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000249513 ENST00000740310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 0 publications found

Genes affected

ENSG00000249513 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0932 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740310.1. 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
	ENSG00000249513	ENST00000740310.1		n.246+135A>C		intron	N/A
	ENSG00000249513	ENST00000740311.1		n.225+135A>C		intron	N/A
	ENSG00000249513	ENST00000740312.1		n.354+135A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0332 AC: 5048 AN: 152088 Hom.: 195 Cov.: 32

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00695

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0333 AC: 5063 AN: 152206 Hom.: 195 Cov.: 32 AF XY: 0.0315 AC XY: 2342 AN XY: 74420

African (AFR) AF: 0.0957 AC: 3973 AN: 41536

American (AMR) AF: 0.0168 AC: 257 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3466

East Asian (EAS) AF: 0.0266 AC: 137 AN: 5152

South Asian (SAS) AF: 0.00994 AC: 48 AN: 4830

European-Finnish (FIN) AF: 0.00188 AC: 20 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00696 AC: 473 AN: 68004

Other (OTH) AF: 0.0279 AC: 59 AN: 2114

Alfa AF: 0.0255 Hom.: 23

Bravo AF: 0.0376

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.085

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: rs7661032;

hg19: chr4-133906532;