rs886038633

Positions:

• chr8-60819981-AACTTTTTTTTTTCCCTTTGGTG-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_017780.4(CHD7):​c.2614-25_2614-4delACTTTTTTTTTTCCCTTTGGTG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHD7 NM_017780.4 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.49

Genes affected

CHD7 (HGNC:20626): (chromodomain helicase DNA binding protein 7) This gene encodes a protein that contains several helicase family domains. Mutations in this gene have been found in some patients with the CHARGE syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 8-60819981-AACTTTTTTTTTTCCCTTTGGTG-A is Benign according to our data. Variant chr8-60819981-AACTTTTTTTTTTCCCTTTGGTG-A is described in ClinVar as [Likely_benign]. Clinvar id is 260896.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHD7	NM_017780.4	c.2614-25_2614-4delACTTTTTTTTTTCCCTTTGGTG		splice_region_variant, intron_variant		ENST00000423902.7	NP_060250.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHD7	ENST00000423902.7	c.2614-25_2614-4delACTTTTTTTTTTCCCTTTGGTG		splice_region_variant, intron_variant		5	NM_017780.4	ENSP00000392028.1
CHD7	ENST00000524602.5	c.1716+38932_1716+38953delACTTTTTTTTTTCCCTTTGGTG		intron_variant		1		ENSP00000437061.1
CHD7	ENST00000525508.1	c.2614-25_2614-4delACTTTTTTTTTTCCCTTTGGTG		splice_region_variant, intron_variant		5		ENSP00000436027.1
CHD7	ENST00000695853.1	n.2614-25_2614-4delACTTTTTTTTTTCCCTTTGGTG		splice_region_variant, intron_variant				ENSP00000512218.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BranchPoint Hunter		6.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886038633; hg19: chr8-61732540;