chr1-196818614-T-G

Variant names:

• chr1-196818614-T-G
• rs436719

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 0.436 in 130,306 control chromosomes in the GnomAD database, including 18,495 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 0.44 (18495 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 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: 0.436 AC: 56815 AN: 130190 Hom.: 18470 Cov.: 23

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.436 AC: 56870 AN: 130306 Hom.: 18495 Cov.: 23 AF XY: 0.437 AC XY: 27678 AN XY: 63330

African (AFR) AF: 0.439 AC: 12366 AN: 28162

American (AMR) AF: 0.535 AC: 7365 AN: 13774

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1609 AN: 3110

East Asian (EAS) AF: 0.523 AC: 2633 AN: 5038

South Asian (SAS) AF: 0.436 AC: 1667 AN: 3824

European-Finnish (FIN) AF: 0.374 AC: 3671 AN: 9812

Middle Eastern (MID) AF: 0.405 AC: 102 AN: 252

European-Non Finnish (NFE) AF: 0.415 AC: 26451 AN: 63672

Other (OTH) AF: 0.478 AC: 850 AN: 1780

Alfa AF: 0.427 Hom.: 2033

Asia WGS AF: 0.494 AC: 1597 AN: 3234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.6
DANN	Benign	0.78
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs436719; hg19: chr1-196787744;