rs4988822

Positions:

• chr6-32431198-C-T

Variant summary

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

The variant allele was found at a frequency of 0.234 in 150,502 control chromosomes in the GnomAD database, including 4,937 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 0.23 (4937 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32431198C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35264 AN: 150386 Hom.: 4935 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.234 AC: 35286 AN: 150502 Hom.: 4937 Cov.: 31 AF XY: 0.237 AC XY: 17402 AN XY: 73502

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.229

Alfa AF: 0.266 Hom.: 1521

Bravo AF: 0.220

Asia WGS AF: 0.203 AC: 710 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	5.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4988822; hg19: chr6-32398975;