5-140369443-G-A

Variant names:

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

Variant summary

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

The NM_031467.3(SLC4A9):​c.2427+784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,052 control chromosomes in the GnomAD database, including 3,389 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 0.20 (3389 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

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>A		intron	N/A	NP_113655.2	Q96Q91-3
	SLC4A9	NM_001258428.2		c.2499+784G>A		intron	N/A	NP_001245357.1	Q96Q91-1
	SLC4A9	NM_001258426.2		c.2385+784G>A		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>A		intron	N/A	ENSP00000424424.1	Q96Q91-3
	SLC4A9	ENST00000507527.1	TSL:1	c.2499+784G>A		intron	N/A	ENSP00000427661.1	Q96Q91-1
	SLC4A9	ENST00000432095.6	TSL:1	c.2385+784G>A		intron	N/A	ENSP00000410056.2	Q96Q91-2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29743 AN: 151934 Hom.: 3381 Cov.: 32

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.196 AC: 29763 AN: 152052 Hom.: 3389 Cov.: 32 AF XY: 0.198 AC XY: 14713 AN XY: 74308

African (AFR) AF: 0.0901 AC: 3738 AN: 41480

American (AMR) AF: 0.218 AC: 3333 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 706 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1489 AN: 5166

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2824 AN: 10560

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15864 AN: 67968

Other (OTH) AF: 0.197 AC: 415 AN: 2108

Alfa AF: 0.219 Hom.: 6273

Bravo AF: 0.185

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.48
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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; COSMIC: COSV50193905; COSMIC: COSV50193905;