7-113271355-A-G

Variant names:

• chr7-113271355-A-G
• rs10953730
• ENST00000811397.1:n.224-7145A>G

Variant summary

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

The ENST00000811397.1(ENSG00000305508):​n.224-7145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,104 control chromosomes in the GnomAD database, including 5,692 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 0.25 (5692 hom., cov: 32)
• Consequence: ENSG00000305508 ENST00000811397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 8 publications found

Genes affected

ENSG00000305508 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811397.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305508	ENST00000811397.1		n.224-7145A>G		intron	N/A
	ENSG00000305508	ENST00000811398.1		n.264-7145A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38387 AN: 151984 Hom.: 5696 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.252 AC: 38376 AN: 152104 Hom.: 5692 Cov.: 32 AF XY: 0.250 AC XY: 18615 AN XY: 74354

African (AFR) AF: 0.101 AC: 4214 AN: 41526

American (AMR) AF: 0.264 AC: 4026 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3470

East Asian (EAS) AF: 0.147 AC: 764 AN: 5186

South Asian (SAS) AF: 0.216 AC: 1038 AN: 4810

European-Finnish (FIN) AF: 0.317 AC: 3347 AN: 10574

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22677 AN: 67956

Other (OTH) AF: 0.288 AC: 606 AN: 2106

Alfa AF: 0.302 Hom.: 23144

Bravo AF: 0.243

Asia WGS AF: 0.164 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.50
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10953730; hg19: chr7-112911410;