rs12106331

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663813.1(ENSG00000287637):​n.187+11697T>C variant causes a intron, non coding transcript 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: ENST00000663813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663813.1	n.187+11697T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.191

Alfa AF: 0.151 Hom.: 1791

Bravo AF: 0.175

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12106331; hg19: chr21-38727277;