2-195891811-GAAA-GA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_018897.3(DNAH7):c.4897-9_4897-8del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,223,982 control chromosomes in the GnomAD database, including 5,971 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.099 (843 hom., cov: 0)
  • Exomes 𝑓: 0.11 (5128 hom.)
• Consequence: DNAH7 NM_018897.3 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10

Genes affected

DNAH7 (HGNC:18661): (dynein axonemal heavy chain 7) DNAH7 is a component of the inner dynein arm of ciliary axonemes (Zhang et al., 2002 [PubMed 11877439]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 2-195891811-GAA-G is Benign according to our data. Variant chr2-195891811-GAA-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH7	NM_018897.3	c.4897-9_4897-8del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000312428.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH7	ENST00000312428.11	c.4897-9_4897-8del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_018897.3	P1

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14736 AN: 149544 Hom.: 840 Cov.: 0

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0531

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00137

Gnomad SAS AF: 0.0784

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.105

GnomAD3 exomes AF: 0.103 AC: 15785 AN: 153394 Hom.: 780 AF XY: 0.105 AC XY: 8726 AN XY: 82892

Gnomad AFR exome AF: 0.180

Gnomad AMR exome AF: 0.0645

Gnomad ASJ exome AF: 0.151

Gnomad EAS exome AF: 0.00283

Gnomad SAS exome AF: 0.108

Gnomad FIN exome AF: 0.0594

Gnomad NFE exome AF: 0.117

Gnomad OTH exome AF: 0.113

GnomAD4 exome AF: 0.108 AC: 116135 AN: 1074328 Hom.: 5128 AF XY: 0.108 AC XY: 57713 AN XY: 533294

Gnomad4 AFR exome AF: 0.172

Gnomad4 AMR exome AF: 0.0710

Gnomad4 ASJ exome AF: 0.147

Gnomad4 EAS exome AF: 0.00151

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.0626

Gnomad4 NFE exome AF: 0.112

Gnomad4 OTH exome AF: 0.105

GnomAD4 genome AF: 0.0986 AC: 14758 AN: 149654 Hom.: 843 Cov.: 0 AF XY: 0.0965 AC XY: 7046 AN XY: 73024

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.00137

Gnomad4 SAS AF: 0.0785

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11292337; hg19: chr2-196756535;