rs788350

Positions:

• chr20-38435993-G-A
• chr20-38435993-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124904958 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904958	XM_047440636.1	c.*505G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0963

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.231

Alfa AF: 0.217 Hom.: 950

Bravo AF: 0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs788350; hg19: chr20-37064636;