rs6702767

Positions:

• chr1-200875419-A-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 0.411 in 152,070 control chromosomes in the GnomAD database, including 14,064 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 0.41 (14064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 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: 0.412 AC: 62531 AN: 151952 Hom.: 14057 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.411 AC: 62571 AN: 152070 Hom.: 14064 Cov.: 32 AF XY: 0.405 AC XY: 30096 AN XY: 74322

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.454

Alfa AF: 0.434 Hom.: 1920

Bravo AF: 0.410

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6702767; hg19: chr1-200844547;