rs4077468

Variant names:

• chr1-205945629-A-G
• rs4077468
• NR_110983.1:n.229+9862A>G

Variant summary

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

The NR_110983.1(SLC26A9-AS1):​n.229+9862A>G variant causes a intron 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_110983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 36 publications found

Genes affected

SLC26A9-AS1 (HGNC:40686): (SLC26A9 and RAB7B antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC26A9-AS1	NR_110983.1	n.229+9862A>G		intron_variant	Intron 2 of 3
SLC26A9-AS1	NR_110984.1	n.201+9862A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.210 AC: 8716 AN: 41504

American (AMR) AF: 0.507 AC: 7753 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1404 AN: 5174

South Asian (SAS) AF: 0.522 AC: 2516 AN: 4822

European-Finnish (FIN) AF: 0.451 AC: 4762 AN: 10554

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27843 AN: 67990

Other (OTH) AF: 0.399 AC: 841 AN: 2110

Alfa AF: 0.388 Hom.: 21639

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

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