chr7-25340079-T-C

Variant names:

• chr7-25340079-T-C
• rs994531
• ENST00000718235.1:n.398+4899A>G

Variant summary

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

The ENST00000718235.1(ENSG00000233824):​n.398+4899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,018 control chromosomes in the GnomAD database, including 20,228 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 (20228 hom., cov: 32)
• Consequence: ENSG00000233824 ENST00000718235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 3 publications found

Genes affected

ENSG00000233824 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375195	XR_927105.2	n.890+8614T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233824	ENST00000718235.1	n.398+4899A>G		intron_variant	Intron 2 of 3
ENSG00000233824	ENST00000765804.1	n.380+4899A>G		intron_variant	Intron 2 of 2
ENSG00000233824	ENST00000765805.1	n.435+4899A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78191 AN: 151900 Hom.: 20210 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.515 AC: 78266 AN: 152018 Hom.: 20228 Cov.: 32 AF XY: 0.514 AC XY: 38198 AN XY: 74300

African (AFR) AF: 0.529 AC: 21928 AN: 41448

American (AMR) AF: 0.510 AC: 7792 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1852 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2731 AN: 5170

South Asian (SAS) AF: 0.447 AC: 2149 AN: 4812

European-Finnish (FIN) AF: 0.470 AC: 4958 AN: 10560

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35045 AN: 67950

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.478 Hom.: 5254

Bravo AF: 0.523

Asia WGS AF: 0.497 AC: 1729 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.26
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs994531; hg19: chr7-25379698; COSMIC: COSV53495416;