rs2880072

Variant names:

• chr6-159404417-G-A
• rs2880072

Your query was ambiguous. Multiple possible variants found:

• chr6-159404417-G-A
• chr6-159404417-G-C
• chr6-159404417-G-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 0.485 in 151,860 control chromosomes in the GnomAD database, including 19,050 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 0.49 (19050 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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: 0.485 AC: 73627 AN: 151740 Hom.: 19020 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.485 AC: 73698 AN: 151860 Hom.: 19050 Cov.: 31 AF XY: 0.485 AC XY: 35980 AN XY: 74192

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.459

Alfa AF: 0.450 Hom.: 2612

Bravo AF: 0.488

Asia WGS AF: 0.540 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2880072; hg19: chr6-159825449;