1-197068107-T-C

Variant names:

• chr1-197068107-T-C
• rs1412631

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 0.762 in 152,082 control chromosomes in the GnomAD database, including 48,511 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 0.76 (48511 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115893 AN: 151964 Hom.: 48492 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.762 AC: 115960 AN: 152082 Hom.: 48511 Cov.: 31 AF XY: 0.768 AC XY: 57126 AN XY: 74354

African (AFR) AF: 0.379 AC: 15709 AN: 41424

American (AMR) AF: 0.864 AC: 13188 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3130 AN: 3468

East Asian (EAS) AF: 0.979 AC: 5052 AN: 5160

South Asian (SAS) AF: 0.898 AC: 4329 AN: 4822

European-Finnish (FIN) AF: 0.929 AC: 9849 AN: 10604

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61878 AN: 68014

Other (OTH) AF: 0.801 AC: 1692 AN: 2112

Alfa AF: 0.761 Hom.: 9424

Bravo AF: 0.741

Asia WGS AF: 0.910 AC: 3164 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.40
DANN	Benign	0.22
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1412631; hg19: chr1-197037237;