XR_927105.2:n.890+8614T>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 XR_927105.2(LOC105375195):​n.890+8614T>C 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: LOC105375195 XR_927105.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718235.1. 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
	ENSG00000233824	ENST00000718235.1		n.398+4899A>G		intron	N/A
	ENSG00000233824	ENST00000765804.1		n.380+4899A>G		intron	N/A
	ENSG00000233824	ENST00000765805.1		n.435+4899A>G		intron	N/A

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 v4.9

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;