chr7-95810675-TG-T

Position:

• chr7-95810675-TG-T

Variant summary

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

The NM_001135556.2(DYNC1I1):​c.223+171del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0938 in 108,610 control chromosomes in the GnomAD database, including 458 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.094 (458 hom., cov: 31)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.791

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 7-95810675-TG-T is Benign according to our data. Variant chr7-95810675-TG-T is described in ClinVar as [Benign]. Clinvar id is 1267410.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNC1I1	NM_001135556.2	c.223+171del		intron_variant		ENST00000447467.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.223+171del		intron_variant		1	NM_001135556.2	P3

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 10183 AN: 108562 Hom.: 459 Cov.: 31

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.00101

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.0938 AC: 10185 AN: 108610 Hom.: 458 Cov.: 31 AF XY: 0.0931 AC XY: 4895 AN XY: 52558

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.00101

Gnomad4 SAS AF: 0.0757

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0746 Hom.: 65

Bravo AF: 0.0641

Asia WGS AF: 0.0240 AC: 82 AN: 3466

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

Jun 03, 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: rs144180774; hg19: chr7-95439987;