7-1164205-G-C

Variant names:

• chr7-1164205-G-C
• ENST00000422230.1:n.175G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000423008.2(ZFAND2A-DT):​n.339G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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)
• Consequence: ZFAND2A-DT ENST00000423008.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

Genes affected

ZFAND2A-DT (HGNC:41187): (ZFAND2A divergent transcript)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFAND2A-DT	NR_110065.1	n.657G>C		non_coding_transcript_exon_variant	Exon 4 of 4
ZFAND2A-DT	NR_110066.1	n.339G>C		non_coding_transcript_exon_variant	Exon 3 of 3
ZFAND2A-DT	NR_110067.1	n.595G>C		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFAND2A-DT	ENST00000422230.1	n.175G>C		non_coding_transcript_exon_variant	Exon 2 of 2	4
ZFAND2A-DT	ENST00000423008.2	n.339G>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
ZFAND2A-DT	ENST00000655003.1	n.363G>C		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.21

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-1203841;