rs10800150

Variant names:

• chr1-165715845-A-G
• rs10800150

Your query was ambiguous. Multiple possible variants found:

• chr1-165715845-A-G
• chr1-165715845-A-T

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 0.249 in 152,010 control chromosomes in the GnomAD database, including 6,263 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 0.25 (6263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 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: 0.249 AC: 37769 AN: 151892 Hom.: 6256 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.249 AC: 37808 AN: 152010 Hom.: 6263 Cov.: 32 AF XY: 0.248 AC XY: 18408 AN XY: 74316

African (AFR) AF: 0.434 AC: 17949 AN: 41404

American (AMR) AF: 0.219 AC: 3344 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3472

East Asian (EAS) AF: 0.608 AC: 3135 AN: 5156

South Asian (SAS) AF: 0.139 AC: 672 AN: 4826

European-Finnish (FIN) AF: 0.178 AC: 1881 AN: 10572

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9576 AN: 67988

Other (OTH) AF: 0.235 AC: 496 AN: 2114

Alfa AF: 0.171 Hom.: 4589

Bravo AF: 0.266

Asia WGS AF: 0.324 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.75
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10800150; hg19: chr1-165685082;