rs1064395

Variant names:

• chr19-19250926-G-A
• rs1064395
• NM_004386.3:c.*1015G>A

Variant summary

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

The NM_004386.3(NCAN):​c.*1015G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,238 control chromosomes in the GnomAD database, including 5,564 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 0.24 (5562 hom., cov: 32)
  • Exomes 𝑓: 0.085 (2 hom.)
• Consequence: NCAN NM_004386.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 90 publications found

Genes affected

NCAN (HGNC:2465): (neurocan) Neurocan is a chondroitin sulfate proteoglycan thought to be involved in the modulation of cell adhesion and migration.[supplied by OMIM, Jul 2002]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004386.3. 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
	NCAN	NM_004386.3	MANE Select	c.*1015G>A		3_prime_UTR	Exon 15 of 15	NP_004377.2	O14594

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCAN	ENST00000252575.11	TSL:1 MANE Select	c.*1015G>A		3_prime_UTR	Exon 15 of 15	ENSP00000252575.4	O14594
	NCAN	ENST00000952495.1		c.*1015G>A		3_prime_UTR	Exon 15 of 15	ENSP00000622554.1
	NCAN	ENST00000927540.1		c.*1015G>A		3_prime_UTR	Exon 15 of 15	ENSP00000597599.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35876 AN: 151942 Hom.: 5537 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.244

GnomAD4 exome AF: 0.0852 AC: 15 AN: 176 Hom.: 2 Cov.: 0 AF XY: 0.109 AC XY: 10 AN XY: 92

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.125 AC: 1 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.125 AC: 6 AN: 48

Middle Eastern (MID) AF: 0.167 AC: 1 AN: 6

European-Non Finnish (NFE) AF: 0.0857 AC: 6 AN: 70

Other (OTH) AF: 0.0294 AC: 1 AN: 34

GnomAD4 genome AF: 0.236 AC: 35939 AN: 152062 Hom.: 5562 Cov.: 32 AF XY: 0.233 AC XY: 17309 AN XY: 74314

African (AFR) AF: 0.439 AC: 18213 AN: 41460

American (AMR) AF: 0.161 AC: 2456 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3472

East Asian (EAS) AF: 0.108 AC: 559 AN: 5184

South Asian (SAS) AF: 0.198 AC: 952 AN: 4806

European-Finnish (FIN) AF: 0.117 AC: 1240 AN: 10578

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11032 AN: 67988

Other (OTH) AF: 0.241 AC: 508 AN: 2104

Alfa AF: 0.184 Hom.: 14423

Bravo AF: 0.246

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.72
DANN	Benign	0.57
PhyloP100		-0.75
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: rs1064395; hg19: chr19-19361735;