chr1-15557249-T-C

Position:

• chr1-15557249-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015291.4(DNAJC16):​c.1024-2277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,116 control chromosomes in the GnomAD database, including 7,475 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 0.29 (7475 hom., cov: 33)
• Consequence: DNAJC16 NM_015291.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

DNAJC16 (HGNC:29157): (DnaJ heat shock protein family (Hsp40) member C16) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC16	NM_015291.4	c.1024-2277T>C		intron_variant		ENST00000375847.8	NP_056106.1
DNAJC16	NM_001287811.2	c.88-2277T>C		intron_variant			NP_001274740.1
DNAJC16	NR_109898.2	n.1153-2277T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC16	ENST00000375847.8	c.1024-2277T>C		intron_variant		1	NM_015291.4	ENSP00000365007	P1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43849 AN: 151998 Hom.: 7439 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.289 AC: 43926 AN: 152116 Hom.: 7475 Cov.: 33 AF XY: 0.286 AC XY: 21252 AN XY: 74394

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.275

Alfa AF: 0.240 Hom.: 2247

Bravo AF: 0.289

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs7533125; hg19: chr1-15883744;