rs2701684

Variant names:

• chr7-107659082-G-A
• rs2701684
• ENST00000440512.4:n.1527C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440512.4(SLC26A4-AS1):​n.1527C>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 ENST00000440512.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC26A4-AS1	NR_028137.1	n.1322C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC26A4-AS1	ENST00000440512.4	n.1527C>T		non_coding_transcript_exon_variant	Exon 3 of 5	3
SLC26A4-AS1	ENST00000658036.1	n.2815C>T		non_coding_transcript_exon_variant	Exon 2 of 2
SLC26A4-AS1	ENST00000662671.1	n.1624C>T		non_coding_transcript_exon_variant	Exon 2 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.190 AC: 7863 AN: 41462

American (AMR) AF: 0.631 AC: 9657 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2135 AN: 3466

East Asian (EAS) AF: 0.439 AC: 2278 AN: 5184

South Asian (SAS) AF: 0.770 AC: 3716 AN: 4828

European-Finnish (FIN) AF: 0.733 AC: 7744 AN: 10570

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45729 AN: 67980

Other (OTH) AF: 0.574 AC: 1209 AN: 2108

Alfa AF: 0.571 Hom.: 9734

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2701684; hg19: chr7-107299527;