rs4489285

chr8-31540605-G-Achr8-31540605-G-Cchr8-31540605-G-T

Variant summary

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

The ENST00000656443.1(ENSG00000287204):n.212+449G>A 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 0.585 in 151,952 control chromosomes in the GnomAD database, including 26,237 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 0.58 (26237 hom., cov: 32)
• Consequence: ENST00000656443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379360	XR_001745704.1	n.1168+449G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656443.1	n.212+449G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88783 AN: 151834 Hom.: 26212 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.585 AC: 88851 AN: 151952 Hom.: 26237 Cov.: 32 AF XY: 0.581 AC XY: 43147 AN XY: 74264

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.618

Alfa AF: 0.579 Hom.: 43099

Bravo AF: 0.583

Asia WGS AF: 0.685 AC: 2378 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	8.2
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4489285; hg19: chr8-31398121;