7-153724234-A-G

Variant names:

• chr7-153724234-A-G
• rs2533241
• ENST00000665842.1:n.387-7783T>C

Variant summary

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

The ENST00000665842.1(ENSG00000287744):​n.387-7783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 150,042 control chromosomes in the GnomAD database, including 21,181 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 0.51 (21181 hom., cov: 28)
• Consequence: ENSG00000287744 ENST00000665842.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 2 publications found

Genes affected

ENSG00000287744 (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 = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287744	ENST00000665842.1	n.387-7783T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 75891 AN: 149928 Hom.: 21126 Cov.: 28

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.507 AC: 76002 AN: 150042 Hom.: 21181 Cov.: 28 AF XY: 0.509 AC XY: 37264 AN XY: 73206

African (AFR) AF: 0.721 AC: 29274 AN: 40592

American (AMR) AF: 0.537 AC: 8100 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1372 AN: 3444

East Asian (EAS) AF: 0.718 AC: 3589 AN: 4996

South Asian (SAS) AF: 0.328 AC: 1545 AN: 4708

European-Finnish (FIN) AF: 0.492 AC: 5113 AN: 10396

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25517 AN: 67534

Other (OTH) AF: 0.476 AC: 991 AN: 2080

Alfa AF: 0.452 Hom.: 2029

Bravo AF: 0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2533241; hg19: chr7-153421319; COSMIC: COSV59609561;