ENST00000748853.1:n.351+21188A>G

Variant names:

• chr8-115284322-A-G
• rs1866939
• ENST00000748853.1:n.351+21188A>G

Variant summary

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

The ENST00000748853.1(ENSG00000297548):​n.351+21188A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0447 in 152,202 control chromosomes in the GnomAD database, including 313 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 0.045 (313 hom., cov: 32)
• Consequence: ENSG00000297548 ENST00000748853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• Publications: 0 publications found

Genes affected

ENSG00000297548 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0986 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
ENSG00000297548	ENST00000748853.1	n.351+21188A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6790 AN: 152084 Hom.: 313 Cov.: 32

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00963

Gnomad OTH AF: 0.0369

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

GnomAD4 genome AF: 0.0447 AC: 6801 AN: 152202 Hom.: 313 Cov.: 32 AF XY: 0.0452 AC XY: 3361 AN XY: 74432

African (AFR) AF: 0.0988 AC: 4102 AN: 41528

American (AMR) AF: 0.0468 AC: 714 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3468

East Asian (EAS) AF: 0.0944 AC: 488 AN: 5172

South Asian (SAS) AF: 0.106 AC: 512 AN: 4822

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10620

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00965 AC: 656 AN: 68010

Other (OTH) AF: 0.0380 AC: 80 AN: 2108

Alfa AF: 0.00212 Hom.: 0

Bravo AF: 0.0502

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.57
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1866939; hg19: chr8-116296551;