chr7-95827886-C-T

Position:

• chr7-95827886-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001135556.2(DYNC1I1):​c.315-171C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 151,904 control chromosomes in the GnomAD database, including 780 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.099 (780 hom., cov: 32)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.41

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 7-95827886-C-T is Benign according to our data. Variant chr7-95827886-C-T is described in ClinVar as [Benign]. Clinvar id is 1221778.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNC1I1	NM_001135556.2	c.315-171C>T		intron_variant		ENST00000447467.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.315-171C>T		intron_variant		1	NM_001135556.2	P3

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 15091 AN: 151786 Hom.: 784 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0980

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0994 AC: 15102 AN: 151904 Hom.: 780 Cov.: 32 AF XY: 0.102 AC XY: 7602 AN XY: 74248

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0612 Hom.: 86

Bravo AF: 0.0943

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.087
DANN	Benign	0.59

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: rs41278815; hg19: chr7-95457198; COSMIC: COSV61461730;