rs5998432

Positions:

• chr22-32349929-C-T

Variant summary

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

The ENST00000701728.1(ENSG00000289873):​n.232+2948G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,234 control chromosomes in the GnomAD database, including 1,305 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 0.12 (1305 hom., cov: 32)
• Consequence: ENST00000701728.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC5A4	XM_006724308.4	c.-4+2909G>A		intron_variant			XP_006724371.1
SLC5A4	XM_011530342.3	c.-122+2909G>A		intron_variant			XP_011528644.1
SLC5A4	XM_011530343.3	c.-4+2948G>A		intron_variant			XP_011528645.1
SLC5A4	XM_017028920.2	c.107+2948G>A		intron_variant			XP_016884409.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701728.1	n.232+2948G>A		intron_variant, non_coding_transcript_variant
	ENST00000701275.1	n.259+2909G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18830 AN: 152116 Hom.: 1296 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.124 AC: 18875 AN: 152234 Hom.: 1305 Cov.: 32 AF XY: 0.121 AC XY: 9008 AN XY: 74432

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0494

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.136

Alfa AF: 0.111 Hom.: 2108

Bravo AF: 0.132

Asia WGS AF: 0.134 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5998432; hg19: chr22-32745916;