rs1202437

chr7-149145466-C-T

Variant summary

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

The ENST00000426851.6(ZNF398):c.-489-8479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,092 control chromosomes in the GnomAD database, including 2,480 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 0.17 (2480 hom., cov: 32)
• Consequence: ZNF398 ENST00000426851.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

Genes affected

ZNF398 (HGNC:18373): (zinc finger protein 398) This gene encodes a member of the Kruppel family of C2H2-type zinc-finger transcription factor proteins. The encoded protein acts as a transcriptional activator. Two transcript variants encoding distinct isoforms have been identified for this gene. Other transcript variants have been described, but their full length sequence has not been determined. [provided by RefSeq, Jul 2008]

LOC107986856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986856	XR_001745398.3	n.1146G>A		non_coding_transcript_exon_variant	2/2
ZNF398	NM_020781.4	c.-489-8479C>T		intron_variant
LOC107986856	XR_007060581.1	n.1266G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF398	ENST00000426851.6	c.-489-8479C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25850 AN: 151974 Hom.: 2474 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.170 AC: 25880 AN: 152092 Hom.: 2480 Cov.: 32 AF XY: 0.164 AC XY: 12185 AN XY: 74350

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0573

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.166

Alfa AF: 0.168 Hom.: 2315

Bravo AF: 0.175

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	11
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1202437; hg19: chr7-148842558; COSMIC: COSV69652947; COSMIC: COSV69652947;