1-104717673-A-G

Variant names:

• chr1-104717673-A-G
• rs10494023

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 0.0374 in 152,038 control chromosomes in the GnomAD database, including 262 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 0.037 (262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 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: 0.0373 AC: 5669 AN: 151920 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00380

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0374 AC: 5681 AN: 152038 Hom.: 262 Cov.: 32 AF XY: 0.0391 AC XY: 2903 AN XY: 74332

African (AFR) AF: 0.0680 AC: 2824 AN: 41522

American (AMR) AF: 0.0736 AC: 1123 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3464

East Asian (EAS) AF: 0.149 AC: 774 AN: 5180

South Asian (SAS) AF: 0.0650 AC: 313 AN: 4816

European-Finnish (FIN) AF: 0.0203 AC: 216 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00382 AC: 259 AN: 67860

Other (OTH) AF: 0.0313 AC: 66 AN: 2112

Alfa AF: 0.00809 Hom.: 5

Bravo AF: 0.0452

Asia WGS AF: 0.109 AC: 378 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.53
DANN	Benign	0.78
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs10494023; hg19: chr1-105260295;