rs231757

Variant names:

• chr2-203888764-T-G
• rs231757
• ENST00000810800.1:n.63+7945T>G

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.63+7945T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,120 control chromosomes in the GnomAD database, including 2,776 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 0.19 (2776 hom., cov: 32)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 8 publications found

Genes affected

ENSG00000305408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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
ENSG00000305408	ENST00000810800.1	n.63+7945T>G		intron_variant	Intron 1 of 2
ENSG00000305408	ENST00000810801.1	n.83+7945T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28532 AN: 152002 Hom.: 2767 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.188 AC: 28568 AN: 152120 Hom.: 2776 Cov.: 32 AF XY: 0.185 AC XY: 13751 AN XY: 74358

African (AFR) AF: 0.213 AC: 8844 AN: 41484

American (AMR) AF: 0.146 AC: 2225 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.114 AC: 591 AN: 5180

South Asian (SAS) AF: 0.0957 AC: 461 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1789 AN: 10570

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13276 AN: 67996

Other (OTH) AF: 0.191 AC: 403 AN: 2112

Alfa AF: 0.190 Hom.: 2296

Bravo AF: 0.189

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs231757; hg19: chr2-204753487;