NM_001135556.2:c.1510-5361C>T

Variant names:

• chr7-96070696-C-T
• rs77909595
• NM_001135556.2:c.1510-5361C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135556.2(DYNC1I1):​c.1510-5361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,196 control chromosomes in the GnomAD database, including 399 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 0.060 (399 hom., cov: 32)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 1 publications found

Genes affected

DYNC1I1 (HGNC:2963): (dynein cytoplasmic 1 intermediate chain 1) Enables spectrin binding activity. Involved in vesicle transport along microtubule. Located in several cellular components, including kinetochore; recycling endosome; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135556.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNC1I1	NM_001135556.2	MANE Select	c.1510-5361C>T		intron	N/A	NP_001129028.1
	DYNC1I1	NM_004411.5		c.1561-5361C>T		intron	N/A	NP_004402.1
	DYNC1I1	NM_001278421.2		c.1501-5361C>T		intron	N/A	NP_001265350.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNC1I1	ENST00000447467.6	TSL:1 MANE Select	c.1510-5361C>T		intron	N/A	ENSP00000392337.2
	DYNC1I1	ENST00000324972.10	TSL:1	c.1561-5361C>T		intron	N/A	ENSP00000320130.6
	DYNC1I1	ENST00000457059.2	TSL:1	c.1510-5361C>T		intron	N/A	ENSP00000412444.1

Frequencies

GnomAD3 genomes AF: 0.0595 AC: 9054 AN: 152078 Hom.: 395 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.00962

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0596 AC: 9077 AN: 152196 Hom.: 399 Cov.: 32 AF XY: 0.0592 AC XY: 4408 AN XY: 74412

African (AFR) AF: 0.125 AC: 5192 AN: 41502

American (AMR) AF: 0.0318 AC: 487 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3468

East Asian (EAS) AF: 0.00964 AC: 50 AN: 5186

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4822

European-Finnish (FIN) AF: 0.0415 AC: 440 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0355 AC: 2416 AN: 68004

Other (OTH) AF: 0.0440 AC: 93 AN: 2116

Alfa AF: 0.0295 Hom.: 36

Bravo AF: 0.0604

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	16
DANN	Benign	0.64
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

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: rs77909595; hg19: chr7-95700008;