rs10490889

Positions:

• chr3-6240341-G-A

Variant summary

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

The ENST00000435651.1(ENSG00000226022):​n.95+91763G>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 0.335 in 152,012 control chromosomes in the GnomAD database, including 8,989 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 0.34 (8989 hom., cov: 33)
• Consequence: ENST00000435651.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435651.1	n.95+91763G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50938 AN: 151894 Hom.: 8981 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.335 AC: 50986 AN: 152012 Hom.: 8989 Cov.: 33 AF XY: 0.337 AC XY: 25010 AN XY: 74298

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.313

Alfa AF: 0.347 Hom.: 1603

Bravo AF: 0.325

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490889; hg19: chr3-6282028;