rs11802371

chr1-247379536-A-Gchr1-247379536-A-T

Variant summary

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

The ENST00000697395.1(ZNF496-DT):n.1181+5393A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,886 control chromosomes in the GnomAD database, including 17,721 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 0.47 (17721 hom., cov: 33)
• Consequence: ZNF496-DT ENST00000697395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

ZNF496-DT (HGNC:55991): (ZNF496 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -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 = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF496-DT	ENST00000697395.1	n.1181+5393A>G		intron_variant, non_coding_transcript_variant
ZNF496-DT	ENST00000697397.1	n.581-13605A>G		intron_variant, non_coding_transcript_variant
ZNF496-DT	ENST00000697406.1	n.108-6984A>G		intron_variant, non_coding_transcript_variant
ZNF496-DT	ENST00000697407.1	n.207+5393A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71510 AN: 151768 Hom.: 17679 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.472 AC: 71621 AN: 151886 Hom.: 17721 Cov.: 33 AF XY: 0.466 AC XY: 34594 AN XY: 74206

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.445

Alfa AF: 0.428 Hom.: 2001

Bravo AF: 0.480

Asia WGS AF: 0.449 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11802371; hg19: chr1-247542838;