rs373552

Variant names:

• chr6-52937230-A-G
• rs373552

Your query was ambiguous. Multiple possible variants found:

• chr6-52937230-A-G
• chr6-52937230-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.182 in 152,122 control chromosomes in the GnomAD database, including 3,302 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 0.18 (3302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27663 AN: 152004 Hom.: 3298 Cov.: 31

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.182 AC: 27656 AN: 152122 Hom.: 3302 Cov.: 31 AF XY: 0.178 AC XY: 13268 AN XY: 74354

African (AFR) AF: 0.0531 AC: 2204 AN: 41526

American (AMR) AF: 0.192 AC: 2938 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3468

East Asian (EAS) AF: 0.0408 AC: 211 AN: 5174

South Asian (SAS) AF: 0.126 AC: 610 AN: 4828

European-Finnish (FIN) AF: 0.218 AC: 2304 AN: 10564

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17705 AN: 67980

Other (OTH) AF: 0.209 AC: 440 AN: 2108

Alfa AF: 0.236 Hom.: 8013

Bravo AF: 0.175

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.54
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs373552; hg19: chr6-52802028;