rs9313969

chr5-163405759-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646617.1(ENSG00000254186):n.322+20044C>T variant causes a intron, non coding transcript 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: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105377700	XR_001742961.2	n.1236+6560C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646617.1	n.322+20044C>T		intron_variant, non_coding_transcript_variant
	ENST00000503504.1	n.355+20044C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.0727

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.387

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9313969; hg19: chr5-162832765;