rs5998391

Positions:

• chr22-32293653-C-G

Variant summary

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

The ENST00000701728.1(ENSG00000289873):​n.233-27301G>C 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 0.478 in 151,564 control chromosomes in the GnomAD database, including 17,455 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 0.48 (17455 hom., cov: 31)
• Consequence: ENST00000701728.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC5A4	XM_006724308.4	c.-3-39440G>C		intron_variant			XP_006724371.1
SLC5A4	XM_011530342.3	c.-121-27301G>C		intron_variant			XP_011528644.1
SLC5A4	XM_011530343.3	c.-3-39440G>C		intron_variant			XP_011528645.1
SLC5A4	XM_017028920.2	c.108-27301G>C		intron_variant			XP_016884409.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701728.1	n.233-27301G>C		intron_variant, non_coding_transcript_variant
	ENST00000701275.1	n.260-27301G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72456 AN: 151444 Hom.: 17437 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.478 AC: 72506 AN: 151564 Hom.: 17455 Cov.: 31 AF XY: 0.481 AC XY: 35591 AN XY: 74024

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.439

Alfa AF: 0.489 Hom.: 2208

Bravo AF: 0.473

Asia WGS AF: 0.410 AC: 1415 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.6
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5998391; hg19: chr22-32689640;