rs7169541

Variant names:

• chr15-93267981-G-C
• rs7169541
• ENST00000667030.1:n.236+8744G>C

Variant summary

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

The ENST00000667030.1(ENSG00000257060):​n.236+8744G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,132 control chromosomes in the GnomAD database, including 7,354 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 0.27 (7354 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000667030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.947
• Publications: 2 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370982	XR_007064770.1	n.1160+8744G>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000667030.1	n.236+8744G>C		intron_variant	Intron 2 of 8
ENSG00000257060	ENST00000791023.1	n.533+36129G>C		intron_variant	Intron 5 of 6
ENSG00000257060	ENST00000791024.1	n.90+36129G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41778 AN: 152014 Hom.: 7352 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.275 AC: 41770 AN: 152132 Hom.: 7354 Cov.: 32 AF XY: 0.273 AC XY: 20288 AN XY: 74352

African (AFR) AF: 0.0725 AC: 3012 AN: 41546

American (AMR) AF: 0.317 AC: 4834 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3468

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5186

South Asian (SAS) AF: 0.230 AC: 1105 AN: 4814

European-Finnish (FIN) AF: 0.390 AC: 4122 AN: 10568

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

European-Non Finnish (NFE) AF: 0.390 AC: 26510 AN: 67968

Other (OTH) AF: 0.279 AC: 588 AN: 2108

Alfa AF: 0.322 Hom.: 1072

Bravo AF: 0.259

Asia WGS AF: 0.141 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.63
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs7169541; hg19: chr15-93811210;