7-12453831-G-A

Variant names:

• chr7-12453831-G-A
• rs847964
• ENST00000732860.1:n.87+17170C>T

Variant summary

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

The ENST00000732860.1(ENSG00000295809):​n.87+17170C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,942 control chromosomes in the GnomAD database, including 985 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 0.10 (985 hom., cov: 32)
• Consequence: ENSG00000295809 ENST00000732860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 0 publications found

Genes affected

ENSG00000295809 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732860.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295809	ENST00000732860.1		n.87+17170C>T		intron	N/A
	ENSG00000295809	ENST00000732861.1		n.133+5054C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15540 AN: 151824 Hom.: 978 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0943

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.102 AC: 15568 AN: 151942 Hom.: 985 Cov.: 32 AF XY: 0.0996 AC XY: 7392 AN XY: 74248

African (AFR) AF: 0.177 AC: 7313 AN: 41412

American (AMR) AF: 0.0843 AC: 1286 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0943 AC: 327 AN: 3466

East Asian (EAS) AF: 0.0613 AC: 317 AN: 5172

South Asian (SAS) AF: 0.0424 AC: 204 AN: 4812

European-Finnish (FIN) AF: 0.0389 AC: 410 AN: 10552

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0773 AC: 5254 AN: 67964

Other (OTH) AF: 0.103 AC: 217 AN: 2110

Alfa AF: 0.0897 Hom.: 89

Bravo AF: 0.111

Asia WGS AF: 0.0620 AC: 216 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.085
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs847964; hg19: chr7-12493457;