8-37080799-C-G

Variant names:

• chr8-37080799-C-G
• rs1111387
• ENST00000744926.1:n.223-4687G>C

Variant summary

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

The ENST00000744926.1(ENSG00000297043):​n.223-4687G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,064 control chromosomes in the GnomAD database, including 42,197 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 (42197 hom., cov: 32)
• Consequence: ENSG00000297043 ENST00000744926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.879
• Publications: 2 publications found

Genes affected

ENSG00000297043 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 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
ENSG00000297043	ENST00000744926.1	n.223-4687G>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111852 AN: 151946 Hom.: 42192 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.736 AC: 111873 AN: 152064 Hom.: 42197 Cov.: 32 AF XY: 0.737 AC XY: 54809 AN XY: 74338

African (AFR) AF: 0.552 AC: 22887 AN: 41426

American (AMR) AF: 0.761 AC: 11640 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2695 AN: 3472

East Asian (EAS) AF: 0.633 AC: 3266 AN: 5160

South Asian (SAS) AF: 0.807 AC: 3884 AN: 4814

European-Finnish (FIN) AF: 0.829 AC: 8769 AN: 10584

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56112 AN: 68008

Other (OTH) AF: 0.741 AC: 1562 AN: 2108

Alfa AF: 0.722 Hom.: 2345

Bravo AF: 0.720

Asia WGS AF: 0.662 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	10
DANN	Benign	0.63
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs1111387; hg19: chr8-36938317;