rs7740686

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901435	XR_007059816.1	n.464A>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;