rs7172832

Variant names:

• chr15-70393164-T-C
• rs7172832
• ENST00000819967.1:n.512+8909T>C

Variant summary

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

The ENST00000819967.1(ENSG00000306658):​n.512+8909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,892 control chromosomes in the GnomAD database, including 15,611 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 0.45 (15611 hom., cov: 31)
• Consequence: ENSG00000306658 ENST00000819967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 publications found

Genes affected

ENSG00000306658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.484 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
ENSG00000306658	ENST00000819967.1	n.512+8909T>C		intron_variant	Intron 2 of 3
ENSG00000306658	ENST00000819968.1	n.377+8909T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67762 AN: 151774 Hom.: 15587 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.447 AC: 67836 AN: 151892 Hom.: 15611 Cov.: 31 AF XY: 0.444 AC XY: 32974 AN XY: 74236

African (AFR) AF: 0.414 AC: 17146 AN: 41438

American (AMR) AF: 0.493 AC: 7527 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1824 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1319 AN: 5174

South Asian (SAS) AF: 0.375 AC: 1808 AN: 4816

European-Finnish (FIN) AF: 0.425 AC: 4463 AN: 10504

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32133 AN: 67928

Other (OTH) AF: 0.470 AC: 989 AN: 2104

Alfa AF: 0.468 Hom.: 2733

Bravo AF: 0.452

Asia WGS AF: 0.335 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7172832; hg19: chr15-70685503;