10-6140460-T-G

Position:

• chr10-6140460-T-G

Variant summary

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

The XR_930619.3(LOC101928080):​n.614+558A>C 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 0.703 in 152,126 control chromosomes in the GnomAD database, including 37,829 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 0.70 (37829 hom., cov: 32)
• Consequence: LOC101928080 XR_930619.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.68

Genes affected

LOC101928080 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928080	XR_930619.3	n.614+558A>C		intron_variant, non_coding_transcript_variant
LOC101928080	XR_930620.3	n.614+558A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106787 AN: 152008 Hom.: 37787 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.703 AC: 106888 AN: 152126 Hom.: 37829 Cov.: 32 AF XY: 0.704 AC XY: 52317 AN XY: 74362

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.706

Alfa AF: 0.677 Hom.: 69934

Bravo AF: 0.708

Asia WGS AF: 0.657 AC: 2286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0070
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3750671; hg19: chr10-6182423;