chr10-6135831-C-T

Position:

• chr10-6135831-C-T

Variant summary

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

The XR_930619.3(LOC101928080):​n.614+5187G>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 0.43 in 151,842 control chromosomes in the GnomAD database, including 14,190 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 0.43 (14190 hom., cov: 32)
• Consequence: LOC101928080 XR_930619.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

Genes affected

LOC101928080 (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 (AMR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928080	XR_930619.3	n.614+5187G>A		intron_variant, non_coding_transcript_variant
LOC101928080	XR_930620.3	n.614+5187G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65284 AN: 151724 Hom.: 14178 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.430 AC: 65338 AN: 151842 Hom.: 14190 Cov.: 32 AF XY: 0.428 AC XY: 31755 AN XY: 74190

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.473

Alfa AF: 0.440 Hom.: 3804

Bravo AF: 0.437

Asia WGS AF: 0.371 AC: 1293 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	9.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4750012; hg19: chr10-6177794;