rs6757804

chr2-150779318-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 0.58 in 151,812 control chromosomes in the GnomAD database, including 25,855 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 0.58 (25855 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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 (AMR) allele frequency at 95% confidence interval = 0.654 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: 0.581 AC: 88072 AN: 151694 Hom.: 25839 Cov.: 30

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.580 AC: 88124 AN: 151812 Hom.: 25855 Cov.: 30 AF XY: 0.575 AC XY: 42656 AN XY: 74154

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.578

Alfa AF: 0.591 Hom.: 44039

Bravo AF: 0.596

Asia WGS AF: 0.598 AC: 2083 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	0.035
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6757804; hg19: chr2-151635832;