Genetic Variant ENST00000422230.1:n.175G>C (chr7-1164205-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000422230.1(ZFAND2A-DT):n.175G>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
ENST00000422230.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.701

Publications

0 publications found

Variant links:

Genes affected

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

ZFAND2A-DT links:

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ACMG classification

Classification was made for transcript

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 (BayesDel_noAF=-1.04).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422230.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ZFAND2A-DT	NR_110065.1	n.657G>C	non_coding_transcript_exon	Exon 4 of 4
ZFAND2A-DT	NR_110066.1	n.339G>C	non_coding_transcript_exon	Exon 3 of 3
ZFAND2A-DT	NR_110067.1	n.595G>C	non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ZFAND2A-DT	ENST00000422230.1	TSL:4	n.175G>C	non_coding_transcript_exon	Exon 2 of 2
ZFAND2A-DT	ENST00000423008.2	TSL:2	n.339G>C	non_coding_transcript_exon	Exon 3 of 3
ZFAND2A-DT	ENST00000655003.1		n.363G>C	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.3

(source)

DANN

Benign

0.21

PhyloP100

-0.70

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over