6-25732074-G-C

Variant names:

• chr6-25732074-G-C
• rs9461209
• ENST00000703602.1:c.*51-5186G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000703602.1(ENSG00000290217):​c.*51-5186G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,170,324 control chromosomes in the GnomAD database, including 90,241 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 0.40 (12515 hom., cov: 34)
  • Exomes 𝑓: 0.38 (77726 hom.)
• Consequence: ENSG00000290217 ENST00000703602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

ENSG00000290217 (HGNC:):

SLC17A1 (HGNC:10929): (solute carrier family 17 member 1) Predicted to enable sialic acid transmembrane transporter activity. Involved in urate metabolic process and urate transport. Located in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

H2BC2P (HGNC:18719): (H2B clustered histone 2, pseudogene) Histones are basic nuclear proteins responsible for nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is a histone pseudogene found on chromosome 6. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A1	XM_017011201.3	c.*3-8281C>G		intron_variant	Intron 12 of 12		XP_016866690.2
H2BC2P		n.25732074G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290217	ENST00000703602.1	c.*51-5186G>C		intron_variant	Intron 11 of 11			ENSP00000515390.1
H2BC2P	ENST00000369177.5	n.89C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60466 AN: 152084 Hom.: 12500 Cov.: 34

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.429

GnomAD4 exome AF: 0.383 AC: 390444 AN: 1018122 Hom.: 77726 Cov.: 13 AF XY: 0.382 AC XY: 193253 AN XY: 505498

Gnomad4 AFR exome AF: 0.463

Gnomad4 AMR exome AF: 0.281

Gnomad4 ASJ exome AF: 0.480

Gnomad4 EAS exome AF: 0.117

Gnomad4 SAS exome AF: 0.361

Gnomad4 FIN exome AF: 0.319

Gnomad4 NFE exome AF: 0.397

Gnomad4 OTH exome AF: 0.380

GnomAD4 genome AF: 0.397 AC: 60492 AN: 152202 Hom.: 12515 Cov.: 34 AF XY: 0.393 AC XY: 29255 AN XY: 74418

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.422

Alfa AF: 0.254 Hom.: 616

Bravo AF: 0.401

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.70
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461209; hg19: chr6-25732302;