rs2571400

chr6-29959945-C-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 0.511 in 145,716 control chromosomes in the GnomAD database, including 18,372 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 0.51 (18372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.591 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: 0.511 AC: 74382 AN: 145612 Hom.: 18354 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.511 AC: 74440 AN: 145716 Hom.: 18372 Cov.: 32 AF XY: 0.512 AC XY: 36498 AN XY: 71234

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.520

Alfa AF: 0.484 Hom.: 9746

Asia WGS AF: 0.588 AC: 2030 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.2
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2571400; hg19: chr6-29927722;