rs708111

Variant names:

• chr1-228003664-G-A
• rs708111

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 0.489 in 151,974 control chromosomes in the GnomAD database, including 18,617 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 0.49 (18617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 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: 0.489 AC: 74235 AN: 151856 Hom.: 18609 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.489 AC: 74272 AN: 151974 Hom.: 18617 Cov.: 32 AF XY: 0.493 AC XY: 36622 AN XY: 74274

African (AFR) AF: 0.368 AC: 15244 AN: 41452

American (AMR) AF: 0.488 AC: 7462 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1869 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2929 AN: 5150

South Asian (SAS) AF: 0.592 AC: 2852 AN: 4816

European-Finnish (FIN) AF: 0.580 AC: 6119 AN: 10550

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36012 AN: 67948

Other (OTH) AF: 0.509 AC: 1072 AN: 2106

Alfa AF: 0.508 Hom.: 2494

Bravo AF: 0.473

Asia WGS AF: 0.580 AC: 2019 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	1.2
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs708111; hg19: chr1-228191365;