chr6-151628177-G-A

Position:

• chr6-151628177-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.1603G>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 0.352 in 152,092 control chromosomes in the GnomAD database, including 10,104 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 (10104 hom., cov: 32)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901435	XR_007059816.1	n.1603G>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53538 AN: 151974 Hom.: 10096 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.352 AC: 53568 AN: 152092 Hom.: 10104 Cov.: 32 AF XY: 0.346 AC XY: 25697 AN XY: 74366

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.375

Alfa AF: 0.326 Hom.: 2754

Bravo AF: 0.365

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.25
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7763637; hg19: chr6-151949312;