chr1-205915146-T-G

Variant names:

• chr1-205915146-T-G
• rs6669481
• ENST00000340781.8:c.2410A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000340781.8(SLC26A9):​c.2410A>C​(p.Arg804Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SLC26A9 ENST00000340781.8 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509
• Publications: 18 publications found

Genes affected

SLC26A9 (HGNC:14469): (solute carrier family 26 member 9) This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length among species) structures yet have markedly different tissue expression patterns. The product of this gene is a highly selective chloride ion channel regulated by WNK kinases. Alternative splicing results in multiple transcript variants encoding differing isoforms.[provided by RefSeq, Dec 2008]

SLC26A9 Gene-Disease associations (from GenCC):

• cystic fibrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC26A9	NM_052934.4	c.*211A>C		3_prime_UTR_variant	Exon 21 of 21	ENST00000367135.8	NP_443166.1
SLC26A9	NM_134325.3	c.2410A>C	p.Arg804Arg	synonymous_variant	Exon 22 of 22		NP_599152.2
SLC26A9	XM_011509121.3	c.*211A>C		3_prime_UTR_variant	Exon 20 of 20		XP_011507423.1
SLC26A9	XM_011509122.3	c.*211A>C		3_prime_UTR_variant	Exon 18 of 18		XP_011507424.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC26A9	ENST00000340781.8	c.2410A>C	p.Arg804Arg	synonymous_variant	Exon 21 of 21	1		ENSP00000341682.4
SLC26A9	ENST00000367135.8	c.*211A>C		3_prime_UTR_variant	Exon 21 of 21	1	NM_052934.4	ENSP00000356103.3
SLC26A9	ENST00000367134.2	c.2410A>C	p.Arg804Arg	synonymous_variant	Exon 22 of 22	5		ENSP00000356102.2
SLC26A9	ENST00000491127.5	n.1971A>C		non_coding_transcript_exon_variant	Exon 13 of 13	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 6162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.41
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.20		Position offset: 37

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

Other links and lift over

dbSNP: rs6669481; hg19: chr1-205884274;