rs11047882

Variant names:

• chr12-25188243-C-G
• rs11047882
• NM_018272.5:c.21+2371G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-25188243-C-G
• chr12-25188243-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018272.5(DNAI7):​c.21+2371G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: DNAI7 NM_018272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 9 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018272.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAI7	NM_018272.5	MANE Select	c.21+2371G>C		intron	N/A	NP_060742.4
	DNAI7	NM_001082973.3		c.3+6833G>C		intron	N/A	NP_001076442.2	Q6TDU7-1
	DNAI7	NM_001082972.3		c.195+2371G>C		intron	N/A	NP_001076441.1	Q6TDU7-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAI7	ENST00000395987.8	TSL:1 MANE Select	c.21+2371G>C		intron	N/A	ENSP00000379310.3	F8W8F9
	DNAI7	ENST00000320267.13	TSL:1	c.3+6833G>C		intron	N/A	ENSP00000313141.9	Q6TDU7-1
	DNAI7	ENST00000354189.9	TSL:1	c.195+2371G>C		intron	N/A	ENSP00000346126.5	Q6TDU7-3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 69698

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.0080
DANN	Benign	0.75
PhyloP100		-2.4

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

Other links and lift over

dbSNP: rs11047882; hg19: chr12-25341177;