20-38435993-G-A

Variant names:

• chr20-38435993-G-A
• rs788350
• XM_047440636.1:c.*505G>A

Variant summary

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

The XM_047440636.1(LOC124904958):​c.*505G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,110 control chromosomes in the GnomAD database, including 7,125 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 0.26 (7125 hom., cov: 32)
• Consequence: LOC124904958 XM_047440636.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 11 publications found

Genes affected

LOC124904958 (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 = 0.51 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: 0.259 AC: 39395 AN: 151990 Hom.: 7099 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.260 AC: 39473 AN: 152110 Hom.: 7125 Cov.: 32 AF XY: 0.257 AC XY: 19086 AN XY: 74348

African (AFR) AF: 0.515 AC: 21356 AN: 41442

American (AMR) AF: 0.172 AC: 2635 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3472

East Asian (EAS) AF: 0.0963 AC: 498 AN: 5170

South Asian (SAS) AF: 0.196 AC: 943 AN: 4822

European-Finnish (FIN) AF: 0.150 AC: 1591 AN: 10610

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10947 AN: 67990

Other (OTH) AF: 0.231 AC: 489 AN: 2114

Alfa AF: 0.224 Hom.: 1035

Bravo AF: 0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs788350; hg19: chr20-37064636;