rs2701684

chr7-107659082-G-A

Variant summary

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

The NR_028137.1(SLC26A4-AS1):n.1322C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,104 control chromosomes in the GnomAD database, including 25,317 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 0.53 (25317 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLC26A4-AS1 NR_028137.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

Genes affected

SLC26A4-AS1 (HGNC:22385): (SLC26A4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC26A4-AS1	NR_028137.1	n.1322C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC26A4-AS1	ENST00000668981.1	n.257+2520C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81051 AN: 151980 Hom.: 25307 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.533 AC: 81085 AN: 152098 Hom.: 25317 Cov.: 33 AF XY: 0.541 AC XY: 40226 AN XY: 74384

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.574

Alfa AF: 0.548 Hom.: 5408

Bravo AF: 0.502

Asia WGS AF: 0.625 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.7
Dann	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2701684; hg19: chr7-107299527;