rs2038864

chr6-40301570-T-Achr6-40301570-T-G

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 0.25 in 152,152 control chromosomes in the GnomAD database, including 4,893 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 0.25 (4893 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 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: 0.250 AC: 37958 AN: 152034 Hom.: 4888 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.250 AC: 37979 AN: 152152 Hom.: 4893 Cov.: 33 AF XY: 0.252 AC XY: 18711 AN XY: 74384

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.268

Alfa AF: 0.263 Hom.: 666

Bravo AF: 0.240

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.34
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038864; hg19: chr6-40269309;