rs10919843

Variant names:

• chr1-200206940-G-A
• rs10919843

Your query was ambiguous. Multiple possible variants found:

• chr1-200206940-G-A
• chr1-200206940-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;