chr1-206989088-T-C

Variant names:

• chr1-206989088-T-C
• rs2791708

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.472 in 152,034 control chromosomes in the GnomAD database, including 18,929 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 0.47 (18929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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: 0.471 AC: 71593 AN: 151916 Hom.: 18878 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.472 AC: 71706 AN: 152034 Hom.: 18929 Cov.: 32 AF XY: 0.465 AC XY: 34574 AN XY: 74310

African (AFR) AF: 0.724 AC: 30058 AN: 41488

American (AMR) AF: 0.455 AC: 6945 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2217 AN: 5174

South Asian (SAS) AF: 0.225 AC: 1083 AN: 4824

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24971 AN: 67952

Other (OTH) AF: 0.502 AC: 1061 AN: 2112

Alfa AF: 0.408 Hom.: 54582

Bravo AF: 0.496

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2791708; hg19: chr1-207162433;