6-81477120-C-T

Position:

• chr6-81477120-C-T

Variant summary

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

The XR_007059658.1(LOC105377871):​n.23233+14371G>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 0.505 in 150,774 control chromosomes in the GnomAD database, including 19,920 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 0.50 (19920 hom., cov: 30)
• Consequence: LOC105377871 XR_007059658.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

Genes affected

LOC105377871 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377871	XR_007059658.1	n.23233+14371G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76119 AN: 150656 Hom.: 19924 Cov.: 30

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.505 AC: 76125 AN: 150774 Hom.: 19920 Cov.: 30 AF XY: 0.504 AC XY: 37048 AN XY: 73562

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.496

Alfa AF: 0.547 Hom.: 10878

Bravo AF: 0.503

Asia WGS AF: 0.452 AC: 1574 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321761; hg19: chr6-82186837;