rs10511276

Positions:

• chr3-109597791-G-A
• chr3-109597791-G-C

Variant summary

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

The variant allele was found at a frequency of 0.319 in 152,050 control chromosomes in the GnomAD database, including 7,978 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 0.32 (7978 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109597791G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01205	ENST00000658412.1	n.351-49764G>A		intron_variant
LINC01205	ENST00000659474.1	n.301+35532G>A		intron_variant
LINC01205	ENST00000663929.1	n.388-49764G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48513 AN: 151930 Hom.: 7969 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.319 AC: 48539 AN: 152050 Hom.: 7978 Cov.: 33 AF XY: 0.317 AC XY: 23525 AN XY: 74324

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.304

Alfa AF: 0.321 Hom.: 15577

Bravo AF: 0.313

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.066
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511276; hg19: chr3-109316638;