1-111104148-G-A

Variant names:

• chr1-111104148-G-A
• rs17026872

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 0.199 in 152,138 control chromosomes in the GnomAD database, including 3,131 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 0.20 (3131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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: 0.199 AC: 30241 AN: 152020 Hom.: 3127 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.199 AC: 30262 AN: 152138 Hom.: 3131 Cov.: 32 AF XY: 0.195 AC XY: 14531 AN XY: 74362

African (AFR) AF: 0.191 AC: 7929 AN: 41502

American (AMR) AF: 0.168 AC: 2566 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 751 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5194

South Asian (SAS) AF: 0.168 AC: 811 AN: 4818

European-Finnish (FIN) AF: 0.224 AC: 2366 AN: 10562

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15152 AN: 67982

Other (OTH) AF: 0.211 AC: 446 AN: 2112

Alfa AF: 0.208 Hom.: 8415

Bravo AF: 0.192

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17026872; hg19: chr1-111646770;