rs12106331

Variant names:

• chr21-37354975-A-G
• rs12106331
• ENST00000663813.1:n.187+11697T>C

Your query was ambiguous. Multiple possible variants found:

• chr21-37354975-A-G
• chr21-37354975-A-T

Variant summary

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

The ENST00000663813.1(ENSG00000287637):​n.187+11697T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,278 control chromosomes in the GnomAD database, including 2,593 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 0.17 (2593 hom., cov: 33)
• Consequence: ENSG00000287637 ENST00000663813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

Genes affected

ENSG00000287637 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663813.1. 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
	ENSG00000287637	ENST00000663813.1		n.187+11697T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26447 AN: 152160 Hom.: 2583 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.174 AC: 26483 AN: 152278 Hom.: 2593 Cov.: 33 AF XY: 0.178 AC XY: 13250 AN XY: 74460

African (AFR) AF: 0.192 AC: 7984 AN: 41534

American (AMR) AF: 0.174 AC: 2656 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3472

East Asian (EAS) AF: 0.361 AC: 1870 AN: 5182

South Asian (SAS) AF: 0.328 AC: 1583 AN: 4828

European-Finnish (FIN) AF: 0.164 AC: 1742 AN: 10612

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9655 AN: 68030

Other (OTH) AF: 0.191 AC: 403 AN: 2114

Alfa AF: 0.154 Hom.: 2444

Bravo AF: 0.175

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.78
PhyloP100		0.35

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: rs12106331;

hg19: chr21-38727277;