rs10919843

chr1-200206940-G-Achr1-200206940-G-T

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 0.482 in 151,908 control chromosomes in the GnomAD database, including 20,527 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 0.48 (20527 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73172 AN: 151790 Hom.: 20481 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.482 AC: 73271 AN: 151908 Hom.: 20527 Cov.: 31 AF XY: 0.486 AC XY: 36065 AN XY: 74212

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.486

Alfa AF: 0.354 Hom.: 19981

Bravo AF: 0.514

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10919843; hg19: chr1-200176068;