12-25108825-T-TAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018272.5(DNAI7):c.1894-3_1894-2insTTTTTTTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0033 (19 hom., cov: 0)
  • Exomes 𝑓: 0.014 (18 hom.)
  • Failed GnomAD Quality Control
• Consequence: DNAI7 NM_018272.5 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.474

Genes affected

DNAI7 (HGNC:29599): (dynein axonemal intermediate chain 7) Predicted to enable beta-tubulin binding activity and microtubule binding activity. Predicted to be located in cilium; cytoplasm; and microtubule cytoskeleton. Predicted to be part of axonemal dynein complex. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-25108825-T-TAAAAAAAA is Benign according to our data. Variant chr12-25108825-T-TAAAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 2642790.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAI7	NM_018272.5	c.1894-3_1894-2insTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000395987.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAI7	ENST00000395987.8	c.1894-3_1894-2insTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_018272.5	A1

Frequencies

GnomAD3 genomes AF: 0.00333 AC: 161 AN: 48410 Hom.: 19 Cov.: 0

Gnomad AFR AF: 0.00105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00111

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.0150

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000122

Gnomad OTH AF: 0.00558

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0138 AC: 782 AN: 56656 Hom.: 18 Cov.: 13 AF XY: 0.0128 AC XY: 365 AN XY: 28422

Gnomad4 AFR exome AF: 0.0186

Gnomad4 AMR exome AF: 0.0119

Gnomad4 ASJ exome AF: 0.00778

Gnomad4 EAS exome AF: 0.0590

Gnomad4 SAS exome AF: 0.0241

Gnomad4 FIN exome AF: 0.00929

Gnomad4 NFE exome AF: 0.00733

Gnomad4 OTH exome AF: 0.0147

GnomAD4 genome AF: 0.00326 AC: 158 AN: 48428 Hom.: 19 Cov.: 0 AF XY: 0.00377 AC XY: 79 AN XY: 20966

Gnomad4 AFR AF: 0.00105

Gnomad4 AMR AF: 0.000741

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000122

Gnomad4 OTH AF: 0.00558

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

DNAI7: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60370851; hg19: chr12-25261759;