rs34670419

Variant names:

• chr7-99533211-G-A
• rs34670419
• ENST00000454175.1:n.*2677G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-99533211-G-A
• chr7-99533211-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000454175.1(ZKSCAN5):​n.*2677G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000197 in 507,952 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000020 (0 hom.)
• Consequence: ZKSCAN5 ENST00000454175.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869
• Publications: 27 publications found

Genes affected

ZKSCAN5 (HGNC:12867): (zinc finger with KRAB and SCAN domains 5) This gene encodes a zinc finger protein of the Kruppel family. The protein contains a SCAN box and a KRAB A domain and may be involved in transcriptional regulation. A similar protein in mouse is differentially expressed in spermatogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZKSCAN5	NM_145102.4	c.*962G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000326775.10	NP_659570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZKSCAN5	ENST00000454175.1	n.*2677G>A		non_coding_transcript_exon_variant	Exon 5 of 5	1		ENSP00000405716.1
ZKSCAN5	ENST00000326775.10	c.*962G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_145102.4	ENSP00000322872.5
ZKSCAN5	ENST00000394170.6	c.*962G>A		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000377725.2
ZKSCAN5	ENST00000454175.1	n.*2677G>A		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000405716.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000769 AC: 1 AN: 130048 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000202

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000197 AC: 1 AN: 507952 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 276380

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 14904

American (AMR) AF: 0.00 AC: 0 AN: 33338

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18684

East Asian (EAS) AF: 0.00 AC: 0 AN: 28290

South Asian (SAS) AF: 0.00 AC: 0 AN: 61402

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29490

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3858

European-Non Finnish (NFE) AF: 0.00000345 AC: 1 AN: 290086

Other (OTH) AF: 0.00 AC: 0 AN: 27900

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.67
PhyloP100		0.87

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: rs34670419; hg19: chr7-99130834;