7-95813093-CTTTTT-CTTTTTTTT

Variant names:

• chr7-95813093-C-CTTT
• rs11452827
• NM_001135556.2:c.224-142_224-140dupTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001135556.2(DYNC1I1):​c.224-142_224-140dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,112,896 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00039 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0013 (3 hom.)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNC1I1	NM_001135556.2	c.224-142_224-140dupTTT		intron_variant	Intron 3 of 16	ENST00000447467.6	NP_001129028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.224-154_224-153insTTT		intron_variant	Intron 3 of 16	1	NM_001135556.2	ENSP00000392337.2

Frequencies

GnomAD3 genomes AF: 0.000392 AC: 55 AN: 140300 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000551

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000144

Gnomad ASJ AF: 0.000591

Gnomad EAS AF: 0.000620

Gnomad SAS AF: 0.000221

Gnomad FIN AF: 0.000141

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00134 AC: 1299 AN: 972596 Hom.: 3 AF XY: 0.00146 AC XY: 708 AN XY: 483964

Gnomad4 AFR exome AF: 0.00742

Gnomad4 AMR exome AF: 0.00241

Gnomad4 ASJ exome AF: 0.00125

Gnomad4 EAS exome AF: 0.00204

Gnomad4 SAS exome AF: 0.00280

Gnomad4 FIN exome AF: 0.00161

Gnomad4 NFE exome AF: 0.00101

Gnomad4 OTH exome AF: 0.00188

GnomAD4 genome AF: 0.000392 AC: 55 AN: 140300 Hom.: 0 Cov.: 0 AF XY: 0.000326 AC XY: 22 AN XY: 67524

Gnomad4 AFR AF: 0.000551

Gnomad4 AMR AF: 0.000144

Gnomad4 ASJ AF: 0.000591

Gnomad4 EAS AF: 0.000620

Gnomad4 SAS AF: 0.000221

Gnomad4 FIN AF: 0.000141

Gnomad4 NFE AF: 0.000382

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;