rs17281921

Positions:

• chr7-103465449-G-C

Variant summary

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

The ENST00000422488.1(SLC26A5-AS1):​n.1365+18781G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,040 control chromosomes in the GnomAD database, including 1,234 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 0.12 (1234 hom., cov: 32)
• Consequence: SLC26A5-AS1 ENST00000422488.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

SLC26A5-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC26A5-AS1	NR_110141.1	n.1365+18781G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC26A5-AS1	ENST00000422488.1	n.1365+18781G>C		intron_variant		1
SLC26A5-AS1	ENST00000660729.1	n.307+18781G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18546 AN: 151922 Hom.: 1224 Cov.: 32

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0955

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.122 AC: 18589 AN: 152040 Hom.: 1234 Cov.: 32 AF XY: 0.124 AC XY: 9225 AN XY: 74328

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0955

Gnomad4 EAS AF: 0.0823

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.119

Alfa AF: 0.129 Hom.: 169

Bravo AF: 0.116

Asia WGS AF: 0.137 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17281921; hg19: chr7-103105896;