rs17286676

Positions:

• chr5-140369443-G-A
• chr5-140369443-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A9	NM_031467.3	c.2427+784G>A		intron_variant		ENST00000506757.7	NP_113655.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A9	ENST00000506757.7	c.2427+784G>A		intron_variant		1	NM_031467.3	ENSP00000424424.1
SLC4A9	ENST00000507527.1	c.2499+784G>A		intron_variant		1		ENSP00000427661.1
SLC4A9	ENST00000432095.6	c.2385+784G>A		intron_variant		1		ENSP00000410056.2
SLC4A9	ENST00000506545.5	c.2238+784G>A		intron_variant		1		ENSP00000422855.1

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

Gnomad4 AFR AF: 0.0901

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.197

Alfa AF: 0.223 Hom.: 4581

Bravo AF: 0.185

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs17286676; hg19: chr5-139749028; COSMIC: COSV50193905; COSMIC: COSV50193905;