rs9375225

Variant names:

• chr6-98140878-G-T
• rs9375225
• ENST00000606913.5:n.240+41608G>T

Variant summary

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

The ENST00000607032.1(ENSG00000271860):​n.410+41608G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,878 control chromosomes in the GnomAD database, including 14,057 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 0.41 (14057 hom., cov: 32)
• Consequence: ENSG00000271860 ENST00000607032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 12 publications found

Genes affected

ENSG00000271860 (HGNC:58964):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607032.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271860	ENST00000606913.5	TSL:5	n.240+41608G>T		intron	N/A
	ENSG00000271860	ENST00000607032.1	TSL:3	n.410+41608G>T		intron	N/A
	ENSG00000271860	ENST00000607823.5	TSL:5	n.352+41608G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62970 AN: 151762 Hom.: 14062 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.415 AC: 62966 AN: 151878 Hom.: 14057 Cov.: 32 AF XY: 0.411 AC XY: 30528 AN XY: 74200

African (AFR) AF: 0.250 AC: 10338 AN: 41398

American (AMR) AF: 0.362 AC: 5526 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1770 AN: 3464

East Asian (EAS) AF: 0.398 AC: 2058 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1411 AN: 4806

European-Finnish (FIN) AF: 0.510 AC: 5362 AN: 10524

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35054 AN: 67936

Other (OTH) AF: 0.417 AC: 879 AN: 2108

Alfa AF: 0.446 Hom.: 2026

Bravo AF: 0.397

Asia WGS AF: 0.283 AC: 987 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.059
DANN	Benign	0.21
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9375225;

hg19: chr6-98588754;