12-25186937-T-G

Position:

• chr12-25186937-T-G

Variant summary

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

The NM_018272.5(DNAI7):​c.21+3677A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,170 control chromosomes in the GnomAD database, including 5,510 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 0.21 (5510 hom., cov: 32)
• Consequence: DNAI7 NM_018272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

Genes affected

DNAI7 (HGNC:29599): (dynein axonemal intermediate chain 7) Predicted to enable beta-tubulin binding activity and microtubule binding activity. Predicted to be located in cilium; cytoplasm; and microtubule cytoskeleton. Predicted to be part of axonemal dynein complex. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAI7	NM_018272.5	c.21+3677A>C		intron_variant		ENST00000395987.8	NP_060742.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAI7	ENST00000395987.8	c.21+3677A>C		intron_variant		1	NM_018272.5	ENSP00000379310	A1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31756 AN: 152052 Hom.: 5477 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.209 AC: 31833 AN: 152170 Hom.: 5510 Cov.: 32 AF XY: 0.204 AC XY: 15149 AN XY: 74420

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.202

Alfa AF: 0.134 Hom.: 1861

Bravo AF: 0.227

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.55
DANN	Benign	0.34

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: rs11836162; hg19: chr12-25339871;