rs9313969

Variant names:

• chr5-163405759-G-A
• rs9313969
• ENST00000503504.2:n.375+20044C>T

Variant summary

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

The ENST00000503504.2(ENSG00000254186):​n.375+20044C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,066 control chromosomes in the GnomAD database, including 11,338 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 0.38 (11338 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000503504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 1 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1236+6560C>T		intron_variant	Intron 1 of 2
LOC105377700	XR_001742962.3	n.206-6031C>T		intron_variant	Intron 2 of 2
LOC105377700	XR_001742963.1	n.1237-6031C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254186	ENST00000503504.2	n.375+20044C>T		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000503615.6	n.351+20044C>T		intron_variant	Intron 3 of 4	5
ENSG00000254186	ENST00000509211.2	n.390+6560C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57052 AN: 151948 Hom.: 11336 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.0722

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.375 AC: 57059 AN: 152066 Hom.: 11338 Cov.: 32 AF XY: 0.367 AC XY: 27309 AN XY: 74344

African (AFR) AF: 0.291 AC: 12074 AN: 41474

American (AMR) AF: 0.395 AC: 6029 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3472

East Asian (EAS) AF: 0.0727 AC: 377 AN: 5184

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4816

European-Finnish (FIN) AF: 0.400 AC: 4225 AN: 10564

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30692 AN: 67960

Other (OTH) AF: 0.387 AC: 817 AN: 2110

Alfa AF: 0.406 Hom.: 1909

Bravo AF: 0.372

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs9313969; hg19: chr5-162832765;