rs186895

chr2-195901785-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018897.3(DNAH7):c.4336-1291G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,752 control chromosomes in the GnomAD database, including 10,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.32 (10040 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: DNAH7 NM_018897.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH7	NM_018897.3	c.4336-1291G>A		intron_variant		ENST00000312428.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH7	ENST00000312428.11	c.4336-1291G>A		intron_variant		1	NM_018897.3	P1
DNAH7	ENST00000475293.1	n.3978G>A		non_coding_transcript_exon_variant	1/3	1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47856 AN: 151634 Hom.: 10006 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.307

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.316 AC: 47947 AN: 151752 Hom.: 10040 Cov.: 32 AF XY: 0.310 AC XY: 22988 AN XY: 74172

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0729

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.309

Alfa AF: 0.237 Hom.: 2386

Bravo AF: 0.333

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2
Dann	Benign	0.71

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: rs186895; hg19: chr2-196766509;