1-111472670-T-C

Variant names:

• chr1-111472670-T-C
• rs12740822

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 152,070 control chromosomes in the GnomAD database, including 19,424 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 (19424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 10 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 (AMR) allele frequency at 95% confidence interval = 0.641 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: 0.472 AC: 71795 AN: 151952 Hom.: 19419 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.472 AC: 71822 AN: 152070 Hom.: 19424 Cov.: 32 AF XY: 0.469 AC XY: 34888 AN XY: 74338

African (AFR) AF: 0.213 AC: 8825 AN: 41468

American (AMR) AF: 0.652 AC: 9964 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2432 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1342 AN: 5184

South Asian (SAS) AF: 0.383 AC: 1843 AN: 4816

European-Finnish (FIN) AF: 0.547 AC: 5772 AN: 10550

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39744 AN: 67972

Other (OTH) AF: 0.521 AC: 1100 AN: 2112

Alfa AF: 0.567 Hom.: 32412

Bravo AF: 0.475

Asia WGS AF: 0.374 AC: 1301 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	1.0
DANN	Benign	0.80
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs12740822; hg19: chr1-112015292; COSMIC: COSV59058892;