7-107713909-GTATTATTAT-G

Position:

• chr7-107713909-GTATTATTAT-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000441.2(SLC26A4):​c.2319+1301_2319+1309delATTATTATT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0017 (1 hom., cov: 0)
• Consequence: SLC26A4 NM_000441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.731

Genes affected

SLC26A4 (HGNC:8818): (solute carrier family 26 member 4) Mutations in this gene are associated with Pendred syndrome, the most common form of syndromic deafness, an autosomal-recessive disease. It is highly homologous to the SLC26A3 gene; they have similar genomic structures and this gene is located 3' of the SLC26A3 gene. The encoded protein has homology to sulfate transporters. [provided by RefSeq, Jul 2008]

SLC26A4 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC26A4	NM_000441.2	c.2319+1301_2319+1309delATTATTATT		intron_variant		ENST00000644269.2	NP_000432.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC26A4	ENST00000644269.2	c.2319+1301_2319+1309delATTATTATT		intron_variant			NM_000441.2	ENSP00000494017.1
SLC26A4	ENST00000492030.2	n.505+1301_505+1309delATTATTATT		intron_variant		5
SLC26A4	ENST00000644846.1	n.*221+1301_*221+1309delATTATTATT		intron_variant				ENSP00000494344.1

Frequencies

GnomAD3 genomes AF: 0.00166 AC: 247 AN: 148928 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00578

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000738

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: 0.00195

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

GnomAD4 genome AF: 0.00167 AC: 249 AN: 149008 Hom.: 1 Cov.: 0 AF XY: 0.00149 AC XY: 108 AN XY: 72610

Gnomad4 AFR AF: 0.00582

Gnomad4 AMR AF: 0.000737

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: 0.00193

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: rs34694220; hg19: chr7-107354354;