chr7-95813093-C-CT

Position:

• chr7-95813093-C-CT

Variant summary

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

The NM_001135556.2(DYNC1I1):​c.224-140dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 1,097,144 control chromosomes in the GnomAD database, including 20,068 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.41 (11975 hom., cov: 0)
  • Exomes 𝑓: 0.32 (8093 hom.)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.361

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 7-95813093-C-CT is Benign according to our data. Variant chr7-95813093-C-CT is described in ClinVar as [Benign]. Clinvar id is 1285939.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNC1I1	NM_001135556.2	c.224-140dup		intron_variant		ENST00000447467.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.224-140dup		intron_variant		1	NM_001135556.2	P3

Frequencies

GnomAD3 genomes AF: 0.410 AC: 57465 AN: 140216 Hom.: 11956 Cov.: 0

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.317 AC: 303736 AN: 956916 Hom.: 8093 AF XY: 0.314 AC XY: 149570 AN XY: 476124

Gnomad4 AFR exome AF: 0.351

Gnomad4 AMR exome AF: 0.332

Gnomad4 ASJ exome AF: 0.284

Gnomad4 EAS exome AF: 0.356

Gnomad4 SAS exome AF: 0.253

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.321

Gnomad4 OTH exome AF: 0.317

GnomAD4 genome AF: 0.410 AC: 57497 AN: 140228 Hom.: 11975 Cov.: 0 AF XY: 0.411 AC XY: 27735 AN XY: 67496

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.409

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: rs11452827; hg19: chr7-95442405;