rs11421911

Variant names:

• chr13-59666357-CAAAAAA-C
• NM_001042517.2:c.*221_*226delTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr13-59666357-CAAAAAA-C
• chr13-59666357-CAAAAAA-CA
• chr13-59666357-CAAAAAA-CAA
• chr13-59666357-CAAAAAA-CAAA
• chr13-59666357-CAAAAAA-CAAAA
• chr13-59666357-CAAAAAA-CAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
• chr13-59666357-CAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

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

The NM_001042517.2(DIAPH3):​c.*221_*226delTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000315 in 190,224 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000032 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DIAPH3 NM_001042517.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

DIAPH3 (HGNC:15480): (diaphanous related formin 3) This gene encodes a member of the diaphanous subfamily of the formin family. Members of this family are involved in actin remodeling and regulate cell movement and adhesion. Mutations in this gene are associated with autosomal dominant auditory neuropathy 1. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIAPH3	NM_001042517.2	c.*221_*226delTTTTTT		3_prime_UTR_variant	Exon 28 of 28	ENST00000400324.9	NP_001035982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIAPH3	ENST00000400324	c.*221_*226delTTTTTT		3_prime_UTR_variant	Exon 28 of 28	1	NM_001042517.2	ENSP00000383178.3
DIAPH3	ENST00000400319.5	c.*221_*226delTTTTTT		downstream_gene_variant		1		ENSP00000383173.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 111942 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000315 AC: 6 AN: 190224 Hom.: 0 AF XY: 0.0000399 AC XY: 4 AN XY: 100166

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000893

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000111

Gnomad4 NFE exome AF: 0.0000325

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 111942 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 52656

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-60240491;