rs2618444

Variant names:

• chr8-11480861-A-C
• rs2618444
• ENST00000644741.1:n.64+144T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-11480861-A-C
• chr8-11480861-A-T

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.64+144T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,096 control chromosomes in the GnomAD database, including 6,450 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 0.26 (6448 hom., cov: 32)
  • Exomes 𝑓: 0.28 (2 hom.)
• Consequence: ENSG00000284957 ENST00000644741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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
ENSG00000284957	ENST00000644741.1	n.64+144T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39246 AN: 151888 Hom.: 6431 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.278 AC: 25 AN: 90 Hom.: 2 AF XY: 0.292 AC XY: 21 AN XY: 72

Gnomad4 AMR exome AF: 0.333

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.263

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.258 AC: 39278 AN: 152006 Hom.: 6448 Cov.: 32 AF XY: 0.266 AC XY: 19759 AN XY: 74298

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.261

Alfa AF: 0.122 Hom.: 202

Bravo AF: 0.273

Asia WGS AF: 0.545 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2618444; hg19: chr8-11338370;