rs921231

Positions:

• chr8-91348168-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052832.4(SLC26A7):​c.1141-3642T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 215,092 control chromosomes in the GnomAD database, including 4,769 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.20 (4099 hom., cov: 33)
  • Exomes 𝑓: 0.14 (670 hom.)
• Consequence: SLC26A7 NM_052832.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

SLC26A7 (HGNC:14467): (solute carrier family 26 member 7) This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in gene structure and protein length yet have markedly different tissue expression patterns. This gene has abundant and specific expression in the kidney. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC26A7	NM_052832.4	c.1141-3642T>C		intron_variant		ENST00000276609.8	NP_439897.1
SLC26A7	NM_001282356.2	c.1141-3642T>C		intron_variant			NP_001269285.1
SLC26A7	NM_001282357.2	c.238-3642T>C		intron_variant			NP_001269286.1
SLC26A7	NM_134266.2	c.1141-3642T>C		intron_variant			NP_599028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC26A7	ENST00000276609.8	c.1141-3642T>C		intron_variant		1	NM_052832.4	ENSP00000276609	P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30593 AN: 152146 Hom.: 4074 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.0211

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.141 AC: 8837 AN: 62826 Hom.: 670 AF XY: 0.141 AC XY: 4316 AN XY: 30714

Gnomad4 AFR exome AF: 0.374

Gnomad4 AMR exome AF: 0.0610

Gnomad4 ASJ exome AF: 0.0692

Gnomad4 EAS exome AF: 0.0205

Gnomad4 SAS exome AF: 0.0932

Gnomad4 FIN exome AF: 0.0556

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.121

GnomAD4 genome AF: 0.201 AC: 30666 AN: 152266 Hom.: 4099 Cov.: 33 AF XY: 0.195 AC XY: 14492 AN XY: 74454

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0845

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.0969

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.184

Alfa AF: 0.153 Hom.: 2653

Bravo AF: 0.214

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
DANN	Benign	0.77

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: rs921231; hg19: chr8-92360396;