chr1-212722631-T-G

Variant names:

• chr1-212722631-T-G
• rs11120005

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 0.662 in 152,082 control chromosomes in the GnomAD database, including 33,676 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 0.66 (33676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 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: 0.662 AC: 100584 AN: 151964 Hom.: 33650 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.662 AC: 100641 AN: 152082 Hom.: 33676 Cov.: 32 AF XY: 0.661 AC XY: 49127 AN XY: 74334

African (AFR) AF: 0.673 AC: 27880 AN: 41454

American (AMR) AF: 0.508 AC: 7762 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2058 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2883 AN: 5176

South Asian (SAS) AF: 0.631 AC: 3039 AN: 4818

European-Finnish (FIN) AF: 0.730 AC: 7708 AN: 10562

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47229 AN: 68006

Other (OTH) AF: 0.616 AC: 1297 AN: 2104

Alfa AF: 0.695 Hom.: 4611

Bravo AF: 0.642

Asia WGS AF: 0.553 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs11120005; hg19: chr1-212895973;