rs915125

Variant names:

• chr6-81753659-C-T
• rs915125
• ENST00000810160.1:n.224-45C>T

Variant summary

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

The ENST00000810160.1(ENSG00000305295):​n.224-45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,130 control chromosomes in the GnomAD database, including 8,842 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 0.34 (8842 hom., cov: 33)
• Consequence: ENSG00000305295 ENST00000810160.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 14 publications found

Genes affected

ENSG00000305295 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 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
ENSG00000305295	ENST00000810160.1	n.224-45C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50986 AN: 152010 Hom.: 8817 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.336 AC: 51053 AN: 152130 Hom.: 8842 Cov.: 33 AF XY: 0.335 AC XY: 24931 AN XY: 74370

African (AFR) AF: 0.419 AC: 17393 AN: 41506

American (AMR) AF: 0.327 AC: 4996 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1539 AN: 5168

South Asian (SAS) AF: 0.365 AC: 1762 AN: 4824

European-Finnish (FIN) AF: 0.301 AC: 3190 AN: 10588

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19626 AN: 67974

Other (OTH) AF: 0.361 AC: 761 AN: 2110

Alfa AF: 0.309 Hom.: 13788

Bravo AF: 0.342

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.3
DANN	Benign	0.78
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs915125; hg19: chr6-82463376;