chr6-151631755-G-A

Position:

• chr6-151631755-G-A

Variant summary

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

The XR_007059816.1(LOC124901435):​n.4647G>A 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 0.8 in 152,202 control chromosomes in the GnomAD database, including 49,308 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 0.80 (49308 hom., cov: 33)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

Genes affected

LOC124901435 (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 = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901435	XR_007059816.1	n.4647G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121617 AN: 152084 Hom.: 49267 Cov.: 33

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.800 AC: 121714 AN: 152202 Hom.: 49308 Cov.: 33 AF XY: 0.799 AC XY: 59418 AN XY: 74392

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.804

Alfa AF: 0.753 Hom.: 68527

Bravo AF: 0.817

Asia WGS AF: 0.817 AC: 2840 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	5.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6908732; hg19: chr6-151952890; COSMIC: COSV60292427;