2-203687247-C-T

Variant names:

• chr2-203687247-C-T
• rs11681040
• ENST00000732639.1:n.648-6066C>T

Variant summary

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

The ENST00000732639.1(ENSG00000295768):​n.648-6066C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 152,188 control chromosomes in the GnomAD database, including 626 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 0.075 (626 hom., cov: 32)
• Consequence: ENSG00000295768 ENST00000732639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 7 publications found

Genes affected

ENSG00000295768 (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 (AMR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732639.1. 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
	ENSG00000295768	ENST00000732639.1		n.648-6066C>T		intron	N/A
	ENSG00000295768	ENST00000732641.1		n.336+1793C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11474 AN: 152070 Hom.: 620 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0755 AC: 11483 AN: 152188 Hom.: 626 Cov.: 32 AF XY: 0.0773 AC XY: 5749 AN XY: 74406

African (AFR) AF: 0.0202 AC: 837 AN: 41532

American (AMR) AF: 0.112 AC: 1705 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0256 AC: 89 AN: 3472

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.0484 AC: 233 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1394 AN: 10582

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6887 AN: 68008

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0714 Hom.: 388

Bravo AF: 0.0697

Asia WGS AF: 0.0250 AC: 87 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	0.016
DANN	Benign	0.33
PhyloP100		-2.1

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: rs11681040;

hg19: chr2-204551970;