ENST00000644741.1:n.64+48G>A

Variant names:

• chr8-11480957-C-T
• rs35393613
• ENST00000644741.1:n.64+48G>A

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.64+48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,772 control chromosomes in the GnomAD database, including 7,659 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 0.29 (7654 hom., cov: 30)
  • Exomes 𝑓: 0.14 (5 hom.)
• Consequence: ENSG00000284957 ENST00000644741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 11 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644741.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284957	ENST00000644741.1		n.64+48G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44429 AN: 151488 Hom.: 7637 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.143 AC: 24 AN: 168 Hom.: 5 Cov.: 0 AF XY: 0.117 AC XY: 15 AN XY: 128

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 4 AN: 8

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.100 AC: 1 AN: 10

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.119 AC: 16 AN: 134

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.293 AC: 44455 AN: 151604 Hom.: 7654 Cov.: 30 AF XY: 0.300 AC XY: 22260 AN XY: 74086

African (AFR) AF: 0.193 AC: 7975 AN: 41382

American (AMR) AF: 0.458 AC: 6980 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3468

East Asian (EAS) AF: 0.739 AC: 3765 AN: 5098

South Asian (SAS) AF: 0.402 AC: 1920 AN: 4774

European-Finnish (FIN) AF: 0.294 AC: 3086 AN: 10486

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19012 AN: 67842

Other (OTH) AF: 0.306 AC: 644 AN: 2108

Alfa AF: 0.136 Hom.: 247

Bravo AF: 0.308

Asia WGS AF: 0.581 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs35393613; hg19: chr8-11338466;