1-233508110-G-C

Variant names:

• chr1-233508110-G-C
• rs10910200

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 0.75 in 152,050 control chromosomes in the GnomAD database, including 42,870 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 0.75 (42870 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.796 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: 0.751 AC: 114030 AN: 151932 Hom.: 42832 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.750 AC: 114113 AN: 152050 Hom.: 42870 Cov.: 31 AF XY: 0.751 AC XY: 55803 AN XY: 74330

African (AFR) AF: 0.714 AC: 29597 AN: 41454

American (AMR) AF: 0.808 AC: 12354 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2678 AN: 3472

East Asian (EAS) AF: 0.660 AC: 3393 AN: 5144

South Asian (SAS) AF: 0.716 AC: 3448 AN: 4816

European-Finnish (FIN) AF: 0.765 AC: 8095 AN: 10576

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52079 AN: 67982

Other (OTH) AF: 0.773 AC: 1636 AN: 2116

Alfa AF: 0.711 Hom.: 2411

Bravo AF: 0.752

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.60
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs10910200; hg19: chr1-233643856; COSMIC: COSV60039784;