rs4077468

chr1-205945629-A-G

Variant summary

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

The NR_110984.1(SLC26A9-AS1):n.201+9862A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,126 control chromosomes in the GnomAD database, including 11,247 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 0.37 (11247 hom., cov: 32)
• Consequence: SLC26A9-AS1 NR_110984.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848

Genes affected

SLC26A9-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC26A9-AS1	NR_110984.1	n.201+9862A>G		intron_variant, non_coding_transcript_variant
SLC26A9-AS1	NR_110983.1	n.229+9862A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55878 AN: 152008 Hom.: 11241 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.367 AC: 55897 AN: 152126 Hom.: 11247 Cov.: 32 AF XY: 0.376 AC XY: 27937 AN XY: 74332

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.399

Alfa AF: 0.407 Hom.: 6026

Bravo AF: 0.360

Asia WGS AF: 0.408 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077468; hg19: chr1-205914757; COSMIC: COSV65640871;