1-91928382-A-G

Variant names:

• chr1-91928382-A-G
• rs11165816

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 0.146 in 152,136 control chromosomes in the GnomAD database, including 2,213 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 0.15 (2213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.920
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.145 AC: 22096 AN: 152018 Hom.: 2200 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0810

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.146 AC: 22139 AN: 152136 Hom.: 2213 Cov.: 32 AF XY: 0.145 AC XY: 10783 AN XY: 74376

African (AFR) AF: 0.257 AC: 10649 AN: 41482

American (AMR) AF: 0.120 AC: 1840 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2022 AN: 5156

South Asian (SAS) AF: 0.155 AC: 750 AN: 4828

European-Finnish (FIN) AF: 0.0810 AC: 859 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5404 AN: 68004

Other (OTH) AF: 0.150 AC: 316 AN: 2112

Alfa AF: 0.0997 Hom.: 510

Bravo AF: 0.155

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.63
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs11165816; hg19: chr1-92393939;