chr1-196818614-T-G

Position:

• chr1-196818614-T-G

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.196818614T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;