6-147392628-A-G

Position:

• chr6-147392628-A-G

Variant summary

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

The XR_007059802.1(LOC124901421):​n.5250T>C 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 0.505 in 151,946 control chromosomes in the GnomAD database, including 19,462 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 (19462 hom., cov: 32)
• Consequence: LOC124901421 XR_007059802.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

Genes affected

LOC124901421 (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 (AMR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901421	XR_007059802.1	n.5250T>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76672 AN: 151828 Hom.: 19457 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.505 AC: 76712 AN: 151946 Hom.: 19462 Cov.: 32 AF XY: 0.501 AC XY: 37230 AN XY: 74254

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.512

Alfa AF: 0.507 Hom.: 2884

Bravo AF: 0.508

Asia WGS AF: 0.426 AC: 1480 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	2.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7765526; hg19: chr6-147713764;