2-195897767-TAAAAAAAA-TAAAAAAAAA

Variant names:

• chr2-195897767-T-TA
• rs61502519
• NM_018897.3:c.4549-3dupT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018897.3(DNAH7):​c.4549-3dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 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: 𝑓 0.016 (29 hom., cov: 16)
  • Exomes 𝑓: 0.13 (1 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0162 AC: 2026 AN: 124940 Hom.: 29 Cov.: 16

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.00402

Gnomad EAS AF: 0.00554

Gnomad SAS AF: 0.00374

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.00435

Gnomad NFE AF: 0.00640

Gnomad OTH AF: 0.0161

GnomAD3 exomes AF: 0.0945 AC: 8789 AN: 93048 Hom.: 4 AF XY: 0.0931 AC XY: 4710 AN XY: 50580

Gnomad AFR exome AF: 0.0590

Gnomad AMR exome AF: 0.135

Gnomad ASJ exome AF: 0.0984

Gnomad EAS exome AF: 0.145

Gnomad SAS exome AF: 0.0910

Gnomad FIN exome AF: 0.0910

Gnomad NFE exome AF: 0.0832

Gnomad OTH exome AF: 0.116

GnomAD4 exome AF: 0.126 AC: 125904 AN: 1001922 Hom.: 1 Cov.: 0 AF XY: 0.126 AC XY: 63620 AN XY: 506304

Gnomad4 AFR exome AF: 0.0674

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.113

Gnomad4 EAS exome AF: 0.160

Gnomad4 SAS exome AF: 0.145

Gnomad4 FIN exome AF: 0.120

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.0162 AC: 2029 AN: 124950 Hom.: 29 Cov.: 16 AF XY: 0.0163 AC XY: 978 AN XY: 59856

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.0375

Gnomad4 ASJ AF: 0.00402

Gnomad4 EAS AF: 0.00556

Gnomad4 SAS AF: 0.00377

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.00640

Gnomad4 OTH AF: 0.0160

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: rs61502519; hg19: chr2-196762491;