rs7175167

Variant names:

• chr15-70233320-C-T
• rs7175167
• ENST00000819627.1:n.231-21708C>T

Variant summary

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

The ENST00000819627.1(ENSG00000306606):​n.231-21708C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,916 control chromosomes in the GnomAD database, including 3,061 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 0.19 (3061 hom., cov: 32)
• Consequence: ENSG00000306606 ENST00000819627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 publications found

Genes affected

ENSG00000306606 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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
ENSG00000306606	ENST00000819627.1	n.231-21708C>T		intron_variant	Intron 1 of 3
ENSG00000306606	ENST00000819628.1	n.182-21708C>T		intron_variant	Intron 1 of 2
ENSG00000306606	ENST00000819629.1	n.147-21708C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28680 AN: 151800 Hom.: 3051 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.189 AC: 28716 AN: 151916 Hom.: 3061 Cov.: 32 AF XY: 0.187 AC XY: 13859 AN XY: 74250

African (AFR) AF: 0.284 AC: 11773 AN: 41394

American (AMR) AF: 0.176 AC: 2691 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3464

East Asian (EAS) AF: 0.160 AC: 828 AN: 5172

South Asian (SAS) AF: 0.0959 AC: 461 AN: 4806

European-Finnish (FIN) AF: 0.137 AC: 1440 AN: 10534

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10203 AN: 67976

Other (OTH) AF: 0.194 AC: 408 AN: 2104

Alfa AF: 0.168 Hom.: 9200

Bravo AF: 0.201

Asia WGS AF: 0.146 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.15
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7175167; hg19: chr15-70525659;