rs4631432

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522244.1(ENSG00000253796):​n.129+1313T>C variant causes a intron, non coding transcript 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: ENST00000522244.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522244.1	n.129+1313T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.660

Alfa AF: 0.654 Hom.: 4694

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4631432; hg19: chr8-110074205;