rs2160847

Variant names:

• chr2-210736392-T-C
• rs2160847
• ENST00000737540.1:n.435+793T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000737540.1(ENSG00000296241):​n.435+793T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,160 control chromosomes in the GnomAD database, including 2,821 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 0.18 (2821 hom., cov: 32)
• Consequence: ENSG00000296241 ENST00000737540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 5 publications found

Genes affected

ENSG00000296241 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737540.1. 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
	ENSG00000296241	ENST00000737540.1		n.435+793T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27885 AN: 152042 Hom.: 2816 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.183 AC: 27901 AN: 152160 Hom.: 2821 Cov.: 32 AF XY: 0.189 AC XY: 14039 AN XY: 74388

African (AFR) AF: 0.105 AC: 4341 AN: 41528

American (AMR) AF: 0.221 AC: 3378 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3470

East Asian (EAS) AF: 0.155 AC: 801 AN: 5178

South Asian (SAS) AF: 0.210 AC: 1010 AN: 4818

European-Finnish (FIN) AF: 0.321 AC: 3399 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13714 AN: 67984

Other (OTH) AF: 0.175 AC: 369 AN: 2114

Alfa AF: 0.191 Hom.: 647

Bravo AF: 0.172

Asia WGS AF: 0.174 AC: 609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.47
PhyloP100		-2.5

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: rs2160847;

hg19: chr2-211601116;