rs6661074

Variant names:

• chr1-205369991-G-A
• rs6661074

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;