NM_018897.3:c.4549-4_4549-3dupTT

Variant names:

• chr2-195897767-T-TAA
• rs61502519
• NM_018897.3:c.4549-4_4549-3dupTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_018897.3(DNAH7):​c.4549-4_4549-3dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 16)
  • Exomes 𝑓: 0.010 (0 hom.)
• Consequence: DNAH7 NM_018897.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00998 (10060/1008282) while in subpopulation SAS AF= 0.0185 (1051/56758). AF 95% confidence interval is 0.0176. There are 0 homozygotes in gnomad4_exome. There are 5160 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH7	NM_018897.3	c.4549-4_4549-3dupTT		splice_region_variant, intron_variant	Intron 28 of 64	ENST00000312428.11	NP_061720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH7	ENST00000312428.11	c.4549-3_4549-2insTT		splice_region_variant, intron_variant	Intron 28 of 64	1	NM_018897.3	ENSP00000311273.6
DNAH7	ENST00000475293.1	n.5482-3_5482-2insTT		splice_region_variant, intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.000112 AC: 14 AN: 124982 Hom.: 0 Cov.: 16

Gnomad AFR AF: 0.000109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000834

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000761

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000711

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0139 AC: 1289 AN: 93048 Hom.: 0 AF XY: 0.0131 AC XY: 664 AN XY: 50580

Gnomad AFR exome AF: 0.00811

Gnomad AMR exome AF: 0.0221

Gnomad ASJ exome AF: 0.0118

Gnomad EAS exome AF: 0.0265

Gnomad SAS exome AF: 0.0125

Gnomad FIN exome AF: 0.00637

Gnomad NFE exome AF: 0.0126

Gnomad OTH exome AF: 0.0181

GnomAD4 exome AF: 0.00998 AC: 10060 AN: 1008282 Hom.: 0 Cov.: 0 AF XY: 0.0101 AC XY: 5160 AN XY: 509836

Gnomad4 AFR exome AF: 0.00561

Gnomad4 AMR exome AF: 0.0175

Gnomad4 ASJ exome AF: 0.00983

Gnomad4 EAS exome AF: 0.0113

Gnomad4 SAS exome AF: 0.0185

Gnomad4 FIN exome AF: 0.00932

Gnomad4 NFE exome AF: 0.00925

Gnomad4 OTH exome AF: 0.00987

GnomAD4 genome AF: 0.000112 AC: 14 AN: 124982 Hom.: 0 Cov.: 16 AF XY: 0.000150 AC XY: 9 AN XY: 59842

Gnomad4 AFR AF: 0.000109

Gnomad4 AMR AF: 0.0000834

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000761

Gnomad4 NFE AF: 0.0000711

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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: rs61502519; hg19: chr2-196762491;