rs2656989

Variant names:

• chr5-82894900-C-T
• rs2656989
• ENST00000718048.1:n.789+13046G>A

Variant summary

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

The ENST00000718048.1(ENSG00000248112):​n.789+13046G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,180 control chromosomes in the GnomAD database, including 2,003 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 0.15 (2003 hom., cov: 33)
• Consequence: ENSG00000248112 ENST00000718048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 3 publications found

Genes affected

ENSG00000248112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 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
ENSG00000248112	ENST00000718048.1	n.789+13046G>A		intron_variant	Intron 4 of 4
ENSG00000248112	ENST00000718049.1	n.389-31740G>A		intron_variant	Intron 1 of 1
ENSG00000248112	ENST00000745102.1	n.233+26062G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23298 AN: 152062 Hom.: 1999 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.153 AC: 23316 AN: 152180 Hom.: 2003 Cov.: 33 AF XY: 0.158 AC XY: 11783 AN XY: 74414

African (AFR) AF: 0.100 AC: 4165 AN: 41548

American (AMR) AF: 0.159 AC: 2428 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1327 AN: 5162

South Asian (SAS) AF: 0.339 AC: 1633 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1689 AN: 10578

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10872 AN: 67982

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.154 Hom.: 250

Bravo AF: 0.148

Asia WGS AF: 0.249 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.2
DANN	Benign	0.71
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2656989; hg19: chr5-82190719; COSMIC: COSV60160527;