rs6661074

chr1-205369991-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.402 in 152,080 control chromosomes in the GnomAD database, including 13,352 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 0.40 (13352 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 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: 0.403 AC: 61171 AN: 151962 Hom.: 13343 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.402 AC: 61201 AN: 152080 Hom.: 13352 Cov.: 33 AF XY: 0.409 AC XY: 30392 AN XY: 74342

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.430

Alfa AF: 0.454 Hom.: 32672

Bravo AF: 0.397

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
Cadd	Benign	18
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6661074; hg19: chr1-205339119;