6-140139871-G-C

Position:

• chr6-140139871-G-C

Variant summary

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

The XR_943069.2(LOC105378025):​n.1195C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,140 control chromosomes in the GnomAD database, including 52,138 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 0.82 (52138 hom., cov: 32)
• Consequence: LOC105378025 XR_943069.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

Genes affected

LOC105378025 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378025	XR_943069.2	n.1195C>G		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124925 AN: 152022 Hom.: 52073 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.822 AC: 125049 AN: 152140 Hom.: 52138 Cov.: 32 AF XY: 0.823 AC XY: 61228 AN XY: 74354

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.809

Alfa AF: 0.690 Hom.: 1962

Bravo AF: 0.838

Asia WGS AF: 0.878 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.53
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169291; hg19: chr6-140461008;