rs331617

Variant names:

• chr20-57064792-T-C
• rs331617
• ENST00000748753.1:n.-148A>G

Variant summary

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

The ENST00000748753.1(ENSG00000297537):​n.-148A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,160 control chromosomes in the GnomAD database, including 3,962 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 0.22 (3962 hom., cov: 32)
• Consequence: ENSG00000297537 ENST00000748753.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 5 publications found

Genes affected

ENSG00000297537 (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 (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748753.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000297537	ENST00000748753.1		n.-148A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33102 AN: 152040 Hom.: 3957 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.218 AC: 33126 AN: 152160 Hom.: 3962 Cov.: 32 AF XY: 0.216 AC XY: 16044 AN XY: 74392

African (AFR) AF: 0.126 AC: 5218 AN: 41540

American (AMR) AF: 0.193 AC: 2945 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3470

East Asian (EAS) AF: 0.161 AC: 833 AN: 5178

South Asian (SAS) AF: 0.161 AC: 774 AN: 4818

European-Finnish (FIN) AF: 0.261 AC: 2761 AN: 10582

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18737 AN: 67972

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.256 Hom.: 17253

Bravo AF: 0.211

Asia WGS AF: 0.167 AC: 581 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	6.3
DANN	Benign	0.66
PhyloP100		-0.059

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs331617;

hg19: chr20-55639848;