chr8-11480861-A-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.333 AC: 2 AN: 6

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.263 AC: 20 AN: 76

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.138 AC: 5712 AN: 41490

American (AMR) AF: 0.442 AC: 6751 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.722 AC: 3715 AN: 5146

South Asian (SAS) AF: 0.359 AC: 1731 AN: 4818

European-Finnish (FIN) AF: 0.272 AC: 2871 AN: 10572

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17223 AN: 67946

Other (OTH) AF: 0.261 AC: 548 AN: 2098

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2618444; hg19: chr8-11338370;