7-95813378-T-TA

Position:

• chr7-95813378-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001135556.2(DYNC1I1):​c.314+56dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.26 (4708 hom., cov: 0)
  • Exomes 𝑓: 0.28 (906 hom.)
  • Failed GnomAD Quality Control
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.299

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 -10 ACMG points.

• BP6: Variant 7-95813378-T-TA is Benign according to our data. Variant chr7-95813378-T-TA is described in ClinVar as [Benign]. Clinvar id is 1279828.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNC1I1	NM_001135556.2	c.314+56dup		intron_variant		ENST00000447467.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.314+56dup		intron_variant		1	NM_001135556.2	P3

Frequencies

GnomAD3 genomes AF: 0.256 AC: 36040 AN: 140986 Hom.: 4700 Cov.: 0

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.251

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.282 AC: 341468 AN: 1211736 Hom.: 906 Cov.: 20 AF XY: 0.280 AC XY: 168225 AN XY: 600220

Gnomad4 AFR exome AF: 0.325

Gnomad4 AMR exome AF: 0.237

Gnomad4 ASJ exome AF: 0.285

Gnomad4 EAS exome AF: 0.216

Gnomad4 SAS exome AF: 0.252

Gnomad4 FIN exome AF: 0.282

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.281

GnomAD4 genome AF: 0.256 AC: 36061 AN: 140998 Hom.: 4708 Cov.: 0 AF XY: 0.253 AC XY: 17225 AN XY: 68078

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.252

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs35397709; hg19: chr7-95442690;