rs1425902

Positions:

• chr8-53206654-G-A
• chr8-53206654-G-T

Variant summary

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

The ENST00000524425.1(ENSG00000254687):​n.465-9645G>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 0.544 in 152,088 control chromosomes in the GnomAD database, including 25,498 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 0.54 (25498 hom., cov: 32)
• Consequence: ENST00000524425.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375836	XR_928877.2	n.434-9645G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000524425.1	n.465-9645G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000529837.1	n.434-9645G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82743 AN: 151970 Hom.: 25499 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.544 AC: 82757 AN: 152088 Hom.: 25498 Cov.: 32 AF XY: 0.545 AC XY: 40532 AN XY: 74358

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.567

Alfa AF: 0.648 Hom.: 43041

Bravo AF: 0.527

Asia WGS AF: 0.593 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1425902; hg19: chr8-54119214;