6-54774193-G-A

Position:

• chr6-54774193-G-A

Variant summary

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

The XR_001744176.3(LOC107986606):​n.95+27544C>T 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 0.352 in 152,012 control chromosomes in the GnomAD database, including 13,618 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 0.35 (13618 hom., cov: 32)
• Consequence: LOC107986606 XR_001744176.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

LOC107986606 (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 = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986606	XR_001744176.3	n.95+27544C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53437 AN: 151894 Hom.: 13579 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.352 AC: 53532 AN: 152012 Hom.: 13618 Cov.: 32 AF XY: 0.345 AC XY: 25638 AN XY: 74332

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.334

Alfa AF: 0.284 Hom.: 1248

Bravo AF: 0.374

Asia WGS AF: 0.275 AC: 958 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6913881; hg19: chr6-54638991; COSMIC: COSV68338957;