12-25108825-T-TAAAAAAAAAAAAAAAAAAAAAAAAAA

Position:

• chr12-25108825-T-TAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_018272.5(DNAI7):​c.1894-3_1894-2insTTTTTTTTTTTTTTTTTTTTTTTTTT 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 0.00076 (7 hom., cov: 0)
  • Exomes 𝑓: 0.0011 (20 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 12-25108825-T-TAAAAAAAAAAAAAAAAAAAAAAAAAA is Benign according to our data. Variant chr12-25108825-T-TAAAAAAAAAAAAAAAAAAAAAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 2642792.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAI7	NM_018272.5	c.1894-3_1894-2insTTTTTTTTTTTTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000395987.8	NP_060742.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAI7	ENST00000395987.8	c.1894-3_1894-2insTTTTTTTTTTTTTTTTTTTTTTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_018272.5	ENSP00000379310	A1

Frequencies

GnomAD3 genomes AF: 0.000764 AC: 37 AN: 48406 Hom.: 7 Cov.: 0

Gnomad AFR AF: 0.00105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000741

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000674

Gnomad SAS AF: 0.00136

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000651

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00111 AC: 63 AN: 56986 Hom.: 20 Cov.: 13 AF XY: 0.00119 AC XY: 34 AN XY: 28566

Gnomad4 AFR exome AF: 0.000400

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00273

Gnomad4 EAS exome AF: 0.00334

Gnomad4 SAS exome AF: 0.000490

Gnomad4 FIN exome AF: 0.000768

Gnomad4 NFE exome AF: 0.000925

Gnomad4 OTH exome AF: 0.00100

GnomAD4 genome AF: 0.000764 AC: 37 AN: 48424 Hom.: 7 Cov.: 0 AF XY: 0.000811 AC XY: 17 AN XY: 20964

Gnomad4 AFR AF: 0.00105

Gnomad4 AMR AF: 0.000741

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000676

Gnomad4 SAS AF: 0.00137

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000651

Gnomad4 OTH AF: 0.00

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

Nov 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;