rs7763637

Variant names:

• chr6-151628177-G-A
• rs7763637
• XR_007059816.1:n.1603G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 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=-0.82).
• 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: 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

African (AFR) AF: 0.481 AC: 19966 AN: 41476

American (AMR) AF: 0.277 AC: 4241 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1170 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1686 AN: 5168

South Asian (SAS) AF: 0.349 AC: 1682 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1862 AN: 10578

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

European-Non Finnish (NFE) AF: 0.321 AC: 21802 AN: 67974

Other (OTH) AF: 0.375 AC: 792 AN: 2114

Alfa AF: 0.334 Hom.: 15155

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	-0.82
CADD	Benign	0.25
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7763637; hg19: chr6-151949312;