rs1202295

Variant names:

• chr6-19928937-A-C
• rs1202295

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 0.372 in 152,014 control chromosomes in the GnomAD database, including 10,797 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 0.37 (10797 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 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: 0.372 AC: 56455 AN: 151894 Hom.: 10783 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.372 AC: 56513 AN: 152014 Hom.: 10797 Cov.: 32 AF XY: 0.363 AC XY: 26942 AN XY: 74310

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.379

Alfa AF: 0.388 Hom.: 1643

Bravo AF: 0.376

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1202295; hg19: chr6-19929168;