chr5-140369443-G-C

Variant names:

• chr5-140369443-G-C
• rs17286676
• NM_031467.3:c.2427+784G>C

Variant summary

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

The NM_031467.3(SLC4A9):​c.2427+784G>C variant causes a intron 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: SLC4A9 NM_031467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 6 publications found

Genes affected

SLC4A9 (HGNC:11035): (solute carrier family 4 member 9) The protein encoded by this gene is a membrane protein involved in anion exchange. Expression of this gene is mostly limited to the kidney. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

ANKHD1-DT (HGNC:55564): (ANKHD1 divergent transcript)

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=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031467.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC4A9	NM_031467.3	MANE Select	c.2427+784G>C		intron	N/A	NP_113655.2	Q96Q91-3
	SLC4A9	NM_001258428.2		c.2499+784G>C		intron	N/A	NP_001245357.1	Q96Q91-1
	SLC4A9	NM_001258426.2		c.2385+784G>C		intron	N/A	NP_001245355.1	Q96Q91-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC4A9	ENST00000506757.7	TSL:1 MANE Select	c.2427+784G>C		intron	N/A	ENSP00000424424.1	Q96Q91-3
	SLC4A9	ENST00000507527.1	TSL:1	c.2499+784G>C		intron	N/A	ENSP00000427661.1	Q96Q91-1
	SLC4A9	ENST00000432095.6	TSL:1	c.2385+784G>C		intron	N/A	ENSP00000410056.2	Q96Q91-2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.41
PhyloP100		0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17286676; hg19: chr5-139749028;