1-91603410-A-G

Variant names:

• chr1-91603410-A-G
• rs1192404

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 0.208 in 152,212 control chromosomes in the GnomAD database, including 3,707 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 0.21 (3707 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.666
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.208 AC: 31577 AN: 152094 Hom.: 3698 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.208 AC: 31618 AN: 152212 Hom.: 3707 Cov.: 33 AF XY: 0.205 AC XY: 15251 AN XY: 74434

African (AFR) AF: 0.304 AC: 12600 AN: 41508

American (AMR) AF: 0.258 AC: 3942 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3472

East Asian (EAS) AF: 0.134 AC: 694 AN: 5184

South Asian (SAS) AF: 0.254 AC: 1224 AN: 4822

European-Finnish (FIN) AF: 0.109 AC: 1156 AN: 10602

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10608 AN: 68012

Other (OTH) AF: 0.201 AC: 425 AN: 2116

Alfa AF: 0.171 Hom.: 4165

Bravo AF: 0.221

Asia WGS AF: 0.203 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.67
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1192404; hg19: chr1-92068967;