rs10510322

Positions:

• chr3-5999642-C-T

Variant summary

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

The ENST00000425894.1(ENSG00000229642):​n.322+36127C>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 0.0781 in 152,170 control chromosomes in the GnomAD database, including 1,323 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 0.078 (1323 hom., cov: 32)
• Consequence: ENST00000425894.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000425894.1	n.322+36127C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11863 AN: 152052 Hom.: 1324 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00416

Gnomad OTH AF: 0.0576

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

GnomAD4 genome AF: 0.0781 AC: 11884 AN: 152170 Hom.: 1323 Cov.: 32 AF XY: 0.0766 AC XY: 5702 AN XY: 74408

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00416

Gnomad4 OTH AF: 0.0565

Alfa AF: 0.0457 Hom.: 106

Bravo AF: 0.0858

Asia WGS AF: 0.0750 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510322; hg19: chr3-6041329;