rs2750097

Variant names:

• chr20-51112593-A-G
• rs2750097
• ENST00000772957.1:n.91-17302A>G

Variant summary

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

The ENST00000772957.1(ENSG00000300609):​n.91-17302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,084 control chromosomes in the GnomAD database, including 9,826 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 0.34 (9826 hom., cov: 32)
• Consequence: ENSG00000300609 ENST00000772957.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 1 publications found

Genes affected

ENSG00000300609 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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
ENSG00000300609	ENST00000772957.1	n.91-17302A>G		intron_variant	Intron 1 of 3
ENSG00000300609	ENST00000772958.1	n.51-17302A>G		intron_variant	Intron 1 of 3
ENSG00000300633	ENST00000773065.1	n.229-1627T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51322 AN: 151966 Hom.: 9819 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.338 AC: 51331 AN: 152084 Hom.: 9826 Cov.: 32 AF XY: 0.343 AC XY: 25515 AN XY: 74344

African (AFR) AF: 0.145 AC: 6034 AN: 41524

American (AMR) AF: 0.359 AC: 5471 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2152 AN: 5168

South Asian (SAS) AF: 0.475 AC: 2291 AN: 4820

European-Finnish (FIN) AF: 0.459 AC: 4852 AN: 10572

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28258 AN: 67954

Other (OTH) AF: 0.345 AC: 730 AN: 2114

Alfa AF: 0.364 Hom.: 2787

Bravo AF: 0.320

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2750097; hg19: chr20-49729130;