rs12407970

Variant names:

• chr1-242841367-T-C
• rs12407970

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 0.121 in 152,126 control chromosomes in the GnomAD database, including 1,696 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 0.12 (1696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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: 0.120 AC: 18309 AN: 152008 Hom.: 1694 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0446

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.0977

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.121 AC: 18339 AN: 152126 Hom.: 1696 Cov.: 32 AF XY: 0.128 AC XY: 9519 AN XY: 74384

African (AFR) AF: 0.170 AC: 7070 AN: 41476

American (AMR) AF: 0.112 AC: 1718 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0446 AC: 155 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2453 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1366 AN: 4816

European-Finnish (FIN) AF: 0.0977 AC: 1035 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0626 AC: 4255 AN: 68010

Other (OTH) AF: 0.113 AC: 238 AN: 2114

Alfa AF: 0.0804 Hom.: 3434

Bravo AF: 0.120

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.56
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs12407970; hg19: chr1-243004669;