rs9651257

Variant names:

• chr1-92919579-T-C
• rs9651257
• NM_001006605.5:c.54+41797A>G

Variant summary

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

The NM_001006605.5(DIPK1A):​c.54+41797A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,114 control chromosomes in the GnomAD database, including 9,613 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 0.35 (9613 hom., cov: 32)
• Consequence: DIPK1A NM_001006605.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 10 publications found

Genes affected

DIPK1A (HGNC:32213): (divergent protein kinase domain 1A) This gene encodes a member of the FAM69 family of cysteine-rich type II transmembrane proteins. These proteins localize to the endoplasmic reticulum but their specific functions are unknown. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIPK1A	NM_001006605.5	c.54+41797A>G		intron_variant	Intron 1 of 4	ENST00000370310.5	NP_001006606.2
DIPK1A	NM_001252269.2	c.54+41797A>G		intron_variant	Intron 1 of 3		NP_001239198.1
DIPK1A	NM_001252270.2	c.54+41797A>G		intron_variant	Intron 1 of 3		NP_001239199.1
DIPK1A	NM_001252273.2	c.54+41797A>G		intron_variant	Intron 1 of 4		NP_001239202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIPK1A	ENST00000370310.5	c.54+41797A>G		intron_variant	Intron 1 of 4	2	NM_001006605.5	ENSP00000359333.4
DIPK1A	ENST00000615519.4	c.54+41797A>G		intron_variant	Intron 1 of 4	1		ENSP00000483279.1
DIPK1A	ENST00000613902.4	c.54+41797A>G		intron_variant	Intron 1 of 3	4		ENSP00000484866.1
DIPK1A	ENST00000616709.4	c.54+41797A>G		intron_variant	Intron 1 of 3	3		ENSP00000482718.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52690 AN: 151996 Hom.: 9602 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.347 AC: 52739 AN: 152114 Hom.: 9613 Cov.: 32 AF XY: 0.342 AC XY: 25442 AN XY: 74338

African (AFR) AF: 0.374 AC: 15526 AN: 41496

American (AMR) AF: 0.325 AC: 4968 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3464

East Asian (EAS) AF: 0.0530 AC: 275 AN: 5184

South Asian (SAS) AF: 0.194 AC: 934 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4068 AN: 10578

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24942 AN: 67970

Other (OTH) AF: 0.361 AC: 763 AN: 2114

Alfa AF: 0.360 Hom.: 12918

Bravo AF: 0.344

Asia WGS AF: 0.183 AC: 636 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.28
PhyloP100		-0.20
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: rs9651257; hg19: chr1-93385136;