rs1202295

Variant names:

• chr6-19928937-A-C
• rs1202295

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 0.372 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.390 AC: 16136 AN: 41426

American (AMR) AF: 0.307 AC: 4698 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3466

East Asian (EAS) AF: 0.129 AC: 665 AN: 5164

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4812

European-Finnish (FIN) AF: 0.280 AC: 2960 AN: 10578

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27662 AN: 67952

Other (OTH) AF: 0.379 AC: 801 AN: 2112

Alfa AF: 0.388 Hom.: 1704

Bravo AF: 0.376

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.1
DANN	Benign	0.82
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1202295; hg19: chr6-19929168;