8-11480378-T-C

Variant names:

• chr8-11480378-T-C
• rs1564267
• ENST00000644741.1:n.248A>G

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.248A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,020 control chromosomes in the GnomAD database, including 42,312 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 0.74 (42299 hom., cov: 31)
  • Exomes 𝑓: 0.72 (13 hom.)
• Consequence: ENSG00000284957 ENST00000644741.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284957	ENST00000644741.1		n.248A>G		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111728 AN: 151862 Hom.: 42277 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.758

GnomAD4 exome AF: 0.725 AC: 29 AN: 40 Hom.: 13 Cov.: 0 AF XY: 0.885 AC XY: 23 AN XY: 26

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) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.867 AC: 26 AN: 30

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.736 AC: 111794 AN: 151980 Hom.: 42299 Cov.: 31 AF XY: 0.730 AC XY: 54240 AN XY: 74272

African (AFR) AF: 0.544 AC: 22501 AN: 41386

American (AMR) AF: 0.830 AC: 12694 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2740 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3849 AN: 5164

South Asian (SAS) AF: 0.789 AC: 3808 AN: 4828

European-Finnish (FIN) AF: 0.693 AC: 7310 AN: 10542

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56439 AN: 67986

Other (OTH) AF: 0.762 AC: 1607 AN: 2110

Alfa AF: 0.798 Hom.: 22643

Bravo AF: 0.738

Asia WGS AF: 0.778 AC: 2705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1564267; hg19: chr8-11337887;