rs10515334

chr5-102721921-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000654003.1(ENSG00000286338):n.840-151G>A 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 0.0232 in 151,884 control chromosomes in the GnomAD database, including 87 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 0.023 (87 hom., cov: 32)
• Consequence: ENST00000654003.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0232 (3523/151884) while in subpopulation AFR AF= 0.0467 (1935/41404). AF 95% confidence interval is 0.045. There are 87 homozygotes in gnomad4. There are 1698 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 86 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379104	XR_948631.4	n.1332-151G>A		intron_variant, non_coding_transcript_variant
LOC105379104	XR_948632.4	n.1161-151G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654003.1	n.840-151G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0232 AC: 3518 AN: 151768 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.00701

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0260

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

GnomAD4 genome AF: 0.0232 AC: 3523 AN: 151884 Hom.: 87 Cov.: 32 AF XY: 0.0229 AC XY: 1698 AN XY: 74228

Gnomad4 AFR AF: 0.0467

Gnomad4 AMR AF: 0.0119

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0331

Gnomad4 FIN AF: 0.00701

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0257

Alfa AF: 0.0259 Hom.: 10

Bravo AF: 0.0246

Asia WGS AF: 0.0160 AC: 59 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	1.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515334; hg19: chr5-102057625;