rs2841307

chr6-100308811-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 0.199 in 152,042 control chromosomes in the GnomAD database, including 3,360 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 0.20 (3360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30256 AN: 151924 Hom.: 3353 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.199 AC: 30304 AN: 152042 Hom.: 3360 Cov.: 32 AF XY: 0.201 AC XY: 14920 AN XY: 74324

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.174

Alfa AF: 0.163 Hom.: 3251

Bravo AF: 0.204

Asia WGS AF: 0.148 AC: 516 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.22
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2841307; hg19: chr6-100756687; COSMIC: COSV69415896;