rs2613675

Variant names:

• chr8-21193724-A-G
• rs2613675
• ENST00000657734.1:n.1326+101410T>C

Variant summary

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

The ENST00000657734.1(ENSG00000254092):​n.1326+101410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,032 control chromosomes in the GnomAD database, including 19,367 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 0.44 (19367 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 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
ENSG00000254092	ENST00000657734.1	n.1326+101410T>C		intron_variant	Intron 2 of 4
ENSG00000254092	ENST00000659453.1	n.1639+101410T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67411 AN: 151914 Hom.: 19317 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.444 AC: 67511 AN: 152032 Hom.: 19367 Cov.: 32 AF XY: 0.440 AC XY: 32699 AN XY: 74336

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.428

Alfa AF: 0.324 Hom.: 18156

Bravo AF: 0.470

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.091
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2613675; hg19: chr8-21051235;