rs9375813

Variant names:

• chr6-131436107-C-A
• rs9375813
• ENST00000702750.2:n.303+4023G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-131436107-C-A
• chr6-131436107-C-T

Variant summary

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

The ENST00000702750.2(ENSG00000290067):​n.303+4023G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,960 control chromosomes in the GnomAD database, including 1,703 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 0.14 (1703 hom., cov: 32)
• Consequence: ENSG00000290067 ENST00000702750.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 8 publications found

Genes affected

ENSG00000290067 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378005	XR_001744344.2	n.275+4023G>T		intron_variant	Intron 3 of 4
LOC105378005	XR_007059769.1	n.526+4023G>T		intron_variant	Intron 2 of 3
LOC105378005	XR_007059770.1	n.542+4023G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290067	ENST00000702750.2	n.303+4023G>T		intron_variant	Intron 3 of 4
ENSG00000290067	ENST00000771190.1	n.292+4023G>T		intron_variant	Intron 3 of 4
ENSG00000290067	ENST00000771191.1	n.298+4023G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20701 AN: 151842 Hom.: 1704 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0915

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.136 AC: 20732 AN: 151960 Hom.: 1703 Cov.: 32 AF XY: 0.135 AC XY: 10037 AN XY: 74276

African (AFR) AF: 0.235 AC: 9731 AN: 41464

American (AMR) AF: 0.127 AC: 1936 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0915 AC: 317 AN: 3466

East Asian (EAS) AF: 0.133 AC: 689 AN: 5166

South Asian (SAS) AF: 0.0502 AC: 242 AN: 4816

European-Finnish (FIN) AF: 0.0915 AC: 966 AN: 10552

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6425 AN: 67924

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.0977 Hom.: 1218

Bravo AF: 0.145

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs9375813; hg19: chr6-131757247;