rs10203748

Variant names:

• chr2-105459653-T-C
• rs10203748
• ENST00000760277.1:n.344-5737A>G

Variant summary

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

The ENST00000760277.1(ENSG00000299064):​n.344-5737A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,974 control chromosomes in the GnomAD database, including 2,961 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 0.18 (2961 hom., cov: 31)
• Consequence: ENSG00000299064 ENST00000760277.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 1 publications found

Genes affected

ENSG00000299064 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000760277.1. 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
	ENSG00000299064	ENST00000760277.1		n.344-5737A>G		intron	N/A
	ENSG00000299064	ENST00000760278.1		n.344-5737A>G		intron	N/A
	ENSG00000299064	ENST00000760279.1		n.117-5737A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27918 AN: 151852 Hom.: 2953 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.184 AC: 27962 AN: 151974 Hom.: 2961 Cov.: 31 AF XY: 0.184 AC XY: 13676 AN XY: 74286

African (AFR) AF: 0.287 AC: 11889 AN: 41436

American (AMR) AF: 0.206 AC: 3140 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.168 AC: 868 AN: 5180

South Asian (SAS) AF: 0.170 AC: 816 AN: 4802

European-Finnish (FIN) AF: 0.135 AC: 1425 AN: 10526

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8896 AN: 67990

Other (OTH) AF: 0.176 AC: 373 AN: 2114

Alfa AF: 0.148 Hom.: 3478

Bravo AF: 0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.48
PhyloP100		-0.40

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: rs10203748;

hg19: chr2-106076110;