20-48572946-C-T

Variant names:

• chr20-48572946-C-T
• rs4810820
• ENST00000775767.1:n.249+2511G>A

Variant summary

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

The ENST00000775767.1(ENSG00000301042):​n.249+2511G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,890 control chromosomes in the GnomAD database, including 30,140 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 0.62 (30140 hom., cov: 31)
• Consequence: ENSG00000301042 ENST00000775767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 3 publications found

Genes affected

ENSG00000301042 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301042	ENST00000775767.1	n.249+2511G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93694 AN: 151770 Hom.: 30119 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.617 AC: 93750 AN: 151890 Hom.: 30140 Cov.: 31 AF XY: 0.621 AC XY: 46067 AN XY: 74222

African (AFR) AF: 0.426 AC: 17640 AN: 41382

American (AMR) AF: 0.697 AC: 10645 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3186 AN: 5148

South Asian (SAS) AF: 0.587 AC: 2820 AN: 4802

European-Finnish (FIN) AF: 0.755 AC: 7964 AN: 10552

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47088 AN: 67958

Other (OTH) AF: 0.616 AC: 1297 AN: 2106

Alfa AF: 0.663 Hom.: 56815

Bravo AF: 0.606

Asia WGS AF: 0.619 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4810820; hg19: chr20-47189484;