1-196818614-T-G

Variant names:

• chr1-196818614-T-G
• rs436719

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.436 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

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.478

Alfa AF: 0.427 Hom.: 2033

Asia WGS AF: 0.494 AC: 1597 AN: 3234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs436719; hg19: chr1-196787744;