rs6908732

Variant names:

• chr6-151631755-G-A
• rs6908732
• XR_007059816.1:n.4647G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-151631755-G-A
• chr6-151631755-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124901435	XR_007059816.1	n.4647G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.926 AC: 38490 AN: 41550

American (AMR) AF: 0.810 AC: 12396 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2397 AN: 3470

East Asian (EAS) AF: 0.912 AC: 4726 AN: 5182

South Asian (SAS) AF: 0.768 AC: 3701 AN: 4822

European-Finnish (FIN) AF: 0.679 AC: 7180 AN: 10570

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50168 AN: 67992

Other (OTH) AF: 0.804 AC: 1702 AN: 2116

Alfa AF: 0.764 Hom.: 165371

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
PhyloP100		0.038

Splicing

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

Other links and lift over

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