chr7-96070696-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNC1I1	NM_001135556.2	c.1510-5361C>T		intron_variant	Intron 14 of 16	ENST00000447467.6	NP_001129028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.1510-5361C>T		intron_variant	Intron 14 of 16	1	NM_001135556.2	ENSP00000392337.2

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.00964

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.0415

Gnomad4 NFE AF: 0.0355

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.00905 Hom.: 4

Bravo AF: 0.0604

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	16
DANN	Benign	0.64

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: rs77909595; hg19: chr7-95700008;