rs4631432

Variant names:

• chr8-109061976-A-G
• rs4631432
• ENST00000522244.1:n.129+1313T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-109061976-A-G
• chr8-109061976-A-T

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.129+1313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,142 control chromosomes in the GnomAD database, including 35,105 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 0.67 (35105 hom., cov: 33)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 1 publications found

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 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
ENSG00000253796	ENST00000522244.1	n.129+1313T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102099 AN: 152024 Hom.: 35062 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.672 AC: 102204 AN: 152142 Hom.: 35105 Cov.: 33 AF XY: 0.676 AC XY: 50239 AN XY: 74372

African (AFR) AF: 0.796 AC: 33062 AN: 41528

American (AMR) AF: 0.749 AC: 11449 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1890 AN: 3472

East Asian (EAS) AF: 0.723 AC: 3738 AN: 5170

South Asian (SAS) AF: 0.714 AC: 3443 AN: 4820

European-Finnish (FIN) AF: 0.590 AC: 6245 AN: 10580

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40165 AN: 67970

Other (OTH) AF: 0.660 AC: 1395 AN: 2114

Alfa AF: 0.659 Hom.: 4938

Bravo AF: 0.689

Asia WGS AF: 0.737 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.67
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4631432; hg19: chr8-110074205;