19-11580994-G-A

Position:

• chr19-11580994-G-A

Variant summary

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

The XR_007067140.1(LOC124904638):​n.106-2423G>A 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 0.0947 in 152,122 control chromosomes in the GnomAD database, including 853 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 0.095 (853 hom., cov: 30)
• Consequence: LOC124904638 XR_007067140.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

Genes affected

LOC124904638 (HGNC:):

ZNF627 (HGNC:30570): (zinc finger protein 627) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904638	XR_007067140.1	n.106-2423G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF627	ENST00000585493.5	c.-94+5641G>A		intron_variant		4		ENSP00000464997
ZNF627	ENST00000593279.5	n.519+5641G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14402 AN: 152004 Hom.: 852 Cov.: 30

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0947 AC: 14401 AN: 152122 Hom.: 853 Cov.: 30 AF XY: 0.0946 AC XY: 7030 AN XY: 74348

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0832

Gnomad4 SAS AF: 0.0900

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.117

Alfa AF: 0.108 Hom.: 124

Bravo AF: 0.0875

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79525531; hg19: chr19-11691809;