rs2735902

Positions:

• chr8-144855985-T-A
• chr8-144855985-T-C

Variant summary

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

The ENST00000664211.1(ENSG00000286681):​n.3071A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0501 in 152,192 control chromosomes in the GnomAD database, including 440 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 0.050 (440 hom., cov: 32)
• Consequence: ENSG00000286681 ENST00000664211.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

ENSG00000286681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.144855985T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286681	ENST00000664211.1	n.3071A>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7599 AN: 152074 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.00763

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0206

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0501 AC: 7619 AN: 152192 Hom.: 440 Cov.: 32 AF XY: 0.0523 AC XY: 3893 AN XY: 74418

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.0340

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.0461

Gnomad4 FIN AF: 0.00763

Gnomad4 NFE AF: 0.0206

Gnomad4 OTH AF: 0.0413

Alfa AF: 0.00995 Hom.: 3

Bravo AF: 0.0612

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2735902; hg19: chr8-146081370;