19-37710811-G-T

Variant names:

• chr19-37710811-G-T
• rs7253081
• NM_032689.5:c.9+799C>A

Variant summary

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

The NM_032689.5(ZNF607):​c.9+799C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,052 control chromosomes in the GnomAD database, including 21,627 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 0.52 (21627 hom., cov: 32)
• Consequence: ZNF607 NM_032689.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 7 publications found

Genes affected

ZNF607 (HGNC:28192): (zinc finger protein 607) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000267552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF607	NM_032689.5	c.9+799C>A		intron_variant	Intron 2 of 4	ENST00000355202.9	NP_116078.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF607	ENST00000355202.9	c.9+799C>A		intron_variant	Intron 2 of 4	2	NM_032689.5	ENSP00000347338.2
ENSG00000267552	ENST00000586606.6	n.9+799C>A		intron_variant	Intron 2 of 6	3		ENSP00000467889.1

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79345 AN: 151934 Hom.: 21594 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.522 AC: 79427 AN: 152052 Hom.: 21627 Cov.: 32 AF XY: 0.522 AC XY: 38799 AN XY: 74338

African (AFR) AF: 0.392 AC: 16264 AN: 41458

American (AMR) AF: 0.528 AC: 8063 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1201 AN: 5176

South Asian (SAS) AF: 0.557 AC: 2686 AN: 4824

European-Finnish (FIN) AF: 0.559 AC: 5906 AN: 10572

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41388 AN: 67974

Other (OTH) AF: 0.548 AC: 1151 AN: 2102

Alfa AF: 0.537 Hom.: 3113

Bravo AF: 0.515

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.93
DANN	Benign	0.36
PhyloP100		-0.035
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: rs7253081; hg19: chr19-38201712;