rs16841387

Variant names:

• chr2-195878196-C-A
• rs16841387
• NM_018897.3:c.5962-1497G>T

Variant summary

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

The NM_018897.3(DNAH7):​c.5962-1497G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,106 control chromosomes in the GnomAD database, including 5,684 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 0.24 (5684 hom., cov: 33)
• Consequence: DNAH7 NM_018897.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH7	NM_018897.3	c.5962-1497G>T		intron_variant	Intron 36 of 64	ENST00000312428.11	NP_061720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH7	ENST00000312428.11	c.5962-1497G>T		intron_variant	Intron 36 of 64	1	NM_018897.3	ENSP00000311273.6

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36024 AN: 151988 Hom.: 5666 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.232

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.237 AC: 36099 AN: 152106 Hom.: 5684 Cov.: 33 AF XY: 0.232 AC XY: 17276 AN XY: 74346

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.233

Alfa AF: 0.177 Hom.: 1577

Bravo AF: 0.252

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.68

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: rs16841387; hg19: chr2-196742920;