7-150563728-C-G

Variant names:

• chr7-150563728-C-G
• rs6959171
• XM_017012936.2:c.56G>C

Variant summary

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

The XM_017012936.2(LOC107986860):​c.56G>C​(p.Gly19Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,058 control chromosomes in the GnomAD database, including 5,068 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5068 hom., cov: 32)
• Consequence: LOC107986860 XM_017012936.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 2 publications found

Genes affected

LOC107986860 (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 = 0.318 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: 0.253 AC: 38416 AN: 151940 Hom.: 5056 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.253 AC: 38466 AN: 152058 Hom.: 5068 Cov.: 32 AF XY: 0.254 AC XY: 18880 AN XY: 74332

African (AFR) AF: 0.323 AC: 13371 AN: 41460

American (AMR) AF: 0.229 AC: 3499 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1619 AN: 5172

South Asian (SAS) AF: 0.230 AC: 1105 AN: 4814

European-Finnish (FIN) AF: 0.239 AC: 2522 AN: 10566

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14810 AN: 67976

Other (OTH) AF: 0.235 AC: 498 AN: 2116

Alfa AF: 0.238 Hom.: 566

Bravo AF: 0.256

Asia WGS AF: 0.259 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.41
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6959171; hg19: chr7-150260816;