rs2735902

Variant names:

• chr8-144855985-T-A
• rs2735902
• ENST00000664211.1:n.3071A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000286681 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664211.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286681	ENST00000664211.1		n.3071A>T		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.0548 AC: 2276 AN: 41512

American (AMR) AF: 0.136 AC: 2077 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1260 AN: 5164

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4818

European-Finnish (FIN) AF: 0.00763 AC: 81 AN: 10622

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0206 AC: 1402 AN: 68014

Other (OTH) AF: 0.0413 AC: 87 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2735902;

hg19: chr8-146081370;