rs13138970

Variant names:

• chr4-154353908-G-A
• rs13138970
• NM_001358235.2:c.2476+12302C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-154353908-G-A
• chr4-154353908-G-T

Variant summary

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

The NM_001358235.2(DCHS2):​c.2476+12302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,074 control chromosomes in the GnomAD database, including 8,481 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 0.30 (8481 hom., cov: 33)
• Consequence: DCHS2 NM_001358235.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 3 publications found

Genes affected

DCHS2 (HGNC:23111): (dachsous cadherin-related 2) This gene encodes a large protein that contains many cadherin domains and likely functions in cell adhesion. Genome-wide association studies suggest that this gene may be important in Alzheimer's disease, compressive strength index, and appendicular lean mass. [provided by RefSeq, May 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001358235.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCHS2	NM_001358235.2	MANE Select	c.2476+12302C>T		intron	N/A	NP_001345164.1
	DCHS2	NM_001142552.2		c.2476+12302C>T		intron	N/A	NP_001136024.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCHS2	ENST00000357232.10	TSL:1 MANE Select	c.2476+12302C>T		intron	N/A	ENSP00000349768.5
	DCHS2	ENST00000339452.2	TSL:1	c.2476+12302C>T		intron	N/A	ENSP00000345062.1
	DCHS2	ENST00000623607.4	TSL:1	n.799+3311C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45874 AN: 151958 Hom.: 8485 Cov.: 33

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.301 AC: 45850 AN: 152074 Hom.: 8481 Cov.: 33 AF XY: 0.303 AC XY: 22535 AN XY: 74322

African (AFR) AF: 0.0821 AC: 3410 AN: 41526

American (AMR) AF: 0.341 AC: 5209 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1264 AN: 5164

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4808

European-Finnish (FIN) AF: 0.400 AC: 4209 AN: 10534

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28206 AN: 67980

Other (OTH) AF: 0.324 AC: 682 AN: 2106

Alfa AF: 0.353 Hom.: 5179

Bravo AF: 0.286

Asia WGS AF: 0.219 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13138970; hg19: chr4-155275060;