rs3018626

Variant names:

• chr11-96717198-G-T
• rs3018626
• ENST00000661755.1:n.146-51391G>T

Variant summary

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

The ENST00000661755.1(ENSG00000254587):​n.146-51391G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,172 control chromosomes in the GnomAD database, including 3,166 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 0.19 (3166 hom., cov: 33)
• Consequence: ENSG00000254587 ENST00000661755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

Genes affected

ENSG00000254587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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
ENSG00000254587	ENST00000661755.1	n.146-51391G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29637 AN: 152054 Hom.: 3161 Cov.: 33

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.195 AC: 29652 AN: 152172 Hom.: 3166 Cov.: 33 AF XY: 0.194 AC XY: 14432 AN XY: 74394

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.218

Alfa AF: 0.233 Hom.: 2024

Bravo AF: 0.182

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3018626; hg19: chr11-96588198;