rs6436652

Variant names:

• chr2-156793445-T-C
• rs6436652
• ENST00000665531.1:n.45+4670T>C

Variant summary

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

The ENST00000665531.1(ENSG00000287048):​n.45+4670T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,118 control chromosomes in the GnomAD database, including 8,747 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 0.33 (8747 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000665531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 4 publications found

Genes affected

ENSG00000287048 (HGNC:58940):

ENSG00000299347 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665531.1. 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
	ENSG00000287048	ENST00000665531.1		n.45+4670T>C		intron	N/A
	ENSG00000287048	ENST00000762469.1		n.158+5507T>C		intron	N/A
	ENSG00000287048	ENST00000762470.1		n.162+5507T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50751 AN: 152000 Hom.: 8741 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.334 AC: 50765 AN: 152118 Hom.: 8747 Cov.: 32 AF XY: 0.331 AC XY: 24625 AN XY: 74350

African (AFR) AF: 0.276 AC: 11443 AN: 41528

American (AMR) AF: 0.281 AC: 4295 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1238 AN: 5178

South Asian (SAS) AF: 0.313 AC: 1510 AN: 4822

European-Finnish (FIN) AF: 0.364 AC: 3846 AN: 10562

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26015 AN: 67974

Other (OTH) AF: 0.326 AC: 688 AN: 2110

Alfa AF: 0.370 Hom.: 14699

Bravo AF: 0.322

Asia WGS AF: 0.277 AC: 964 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		0.26

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: rs6436652;

hg19: chr2-157649957;