chr6-151627038-A-T

Variant names:

• chr6-151627038-A-T
• rs7740686
• XR_007059816.1:n.464A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007059816.1(LOC124901435):​n.464A>T 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 152,036 control chromosomes in the GnomAD database, including 10,093 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 (10093 hom., cov: 32)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 16 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53494 AN: 151918 Hom.: 10085 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.352 AC: 53524 AN: 152036 Hom.: 10093 Cov.: 32 AF XY: 0.345 AC XY: 25663 AN XY: 74326

African (AFR) AF: 0.481 AC: 19945 AN: 41436

American (AMR) AF: 0.277 AC: 4234 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3470

East Asian (EAS) AF: 0.326 AC: 1682 AN: 5160

South Asian (SAS) AF: 0.348 AC: 1681 AN: 4824

European-Finnish (FIN) AF: 0.176 AC: 1857 AN: 10580

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21797 AN: 67978

Other (OTH) AF: 0.375 AC: 791 AN: 2108

Alfa AF: 0.328 Hom.: 1045

Bravo AF: 0.365

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.49
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs7740686; hg19: chr6-151948173; COSMIC: COSV69631258;