rs5753917

Positions:

• chr22-32287178-G-A

Variant summary

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

The ENST00000701728.1(ENSG00000289873):​n.233-20826C>T 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 0.283 in 152,012 control chromosomes in the GnomAD database, including 6,124 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 0.28 (6124 hom., cov: 32)
• Consequence: ENST00000701728.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC5A4	XM_006724308.4	c.-3-32965C>T		intron_variant
SLC5A4	XM_011530342.3	c.-121-20826C>T		intron_variant
SLC5A4	XM_011530343.3	c.-3-32965C>T		intron_variant
SLC5A4	XM_017028920.2	c.108-20826C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701728.1	n.233-20826C>T		intron_variant, non_coding_transcript_variant
	ENST00000701275.1	n.260-20826C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42916 AN: 151894 Hom.: 6114 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 42949 AN: 152012 Hom.: 6124 Cov.: 32 AF XY: 0.284 AC XY: 21113 AN XY: 74310

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.265

Alfa AF: 0.266 Hom.: 1341

Bravo AF: 0.279

Asia WGS AF: 0.294 AC: 1019 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	0.20
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5753917; hg19: chr22-32683165;