chr1-196650372-T-C

Variant names:

• chr1-196650372-T-C
• rs505102

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 0.398 in 152,068 control chromosomes in the GnomAD database, including 15,379 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 0.40 (15379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60389 AN: 151950 Hom.: 15331 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.398 AC: 60503 AN: 152068 Hom.: 15379 Cov.: 32 AF XY: 0.399 AC XY: 29631 AN XY: 74344

African (AFR) AF: 0.722 AC: 29963 AN: 41480

American (AMR) AF: 0.389 AC: 5946 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2106 AN: 5148

South Asian (SAS) AF: 0.310 AC: 1498 AN: 4828

European-Finnish (FIN) AF: 0.297 AC: 3137 AN: 10580

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15849 AN: 67960

Other (OTH) AF: 0.357 AC: 753 AN: 2112

Alfa AF: 0.352 Hom.: 7856

Bravo AF: 0.419

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.31
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs505102; hg19: chr1-196619502;