rs11292337

Variant names:

• chr2-195891811-GAAA-G
• rs11292337
• NM_018897.3:c.4897-10_4897-8delTTT

Your query was ambiguous. Multiple possible variants found:

• chr2-195891811-GAAA-G
• chr2-195891811-GAAA-GA
• chr2-195891811-GAAA-GAA
• chr2-195891811-GAAA-GAAAA
• chr2-195891811-GAAA-GAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_018897.3(DNAH7):​c.4897-10_4897-8delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000251 in 1,077,366 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000025 (0 hom.)
• Consequence: DNAH7 NM_018897.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 3 publications found

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]

DNAH7 Gene-Disease associations (from GenCC):

• ciliary dyskinesia, primary, 50

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: LIMITED Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH7	NM_018897.3	c.4897-10_4897-8delTTT		splice_region_variant, intron_variant	Intron 30 of 64	ENST00000312428.11	NP_061720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH7	ENST00000312428.11	c.4897-10_4897-8delTTT		splice_region_variant, intron_variant	Intron 30 of 64	1	NM_018897.3	ENSP00000311273.6

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.0000130 AC: 2 AN: 153394 AF XY: 0.0000121

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000596

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000136

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000251 AC: 27 AN: 1077366 Hom.: 0 AF XY: 0.0000280 AC XY: 15 AN XY: 534816

African (AFR) AF: 0.0000379 AC: 1 AN: 26376

American (AMR) AF: 0.0000402 AC: 1 AN: 24898

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19068

East Asian (EAS) AF: 0.00 AC: 0 AN: 28480

South Asian (SAS) AF: 0.0000376 AC: 2 AN: 53260

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 42934

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4634

European-Non Finnish (NFE) AF: 0.0000276 AC: 23 AN: 832902

Other (OTH) AF: 0.00 AC: 0 AN: 44814

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 3816

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11292337; hg19: chr2-196756535;