rs2108661

Variant names:

• chr5-144939990-A-T
• rs2108661
• ENST00000659832.1:n.182+26746T>A

Variant summary

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

The ENST00000659832.1(ENSG00000251031):​n.182+26746T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 150,314 control chromosomes in the GnomAD database, including 7,170 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 0.31 (7170 hom., cov: 31)
• Consequence: ENSG00000251031 ENST00000659832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

ENSG00000251031 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 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
ENSG00000251031	ENST00000659832.1	n.182+26746T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 45928 AN: 150212 Hom.: 7169 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.306 AC: 45934 AN: 150314 Hom.: 7170 Cov.: 31 AF XY: 0.305 AC XY: 22363 AN XY: 73346

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.308

Alfa AF: 0.132 Hom.: 215

Bravo AF: 0.308

Asia WGS AF: 0.257 AC: 893 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2108661; hg19: chr5-144319553;