rs2074488

Positions:

• chr6-31272654-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 0.127 in 152,212 control chromosomes in the GnomAD database, including 1,423 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 0.13 (1423 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19320 AN: 152094 Hom.: 1419 Cov.: 33

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.0886

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

GnomAD4 genome AF: 0.127 AC: 19331 AN: 152212 Hom.: 1423 Cov.: 33 AF XY: 0.130 AC XY: 9688 AN XY: 74418

Gnomad4 AFR AF: 0.0904

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.0886

Alfa AF: 0.121 Hom.: 105

Bravo AF: 0.120

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2074488; hg19: chr6-31240431;