1-221302557-A-G

Variant names:

• chr1-221302557-A-G
• rs75849835

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0211 in 152,336 control chromosomes in the GnomAD database, including 59 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 0.021 (59 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0211 (3218/152336) while in subpopulation SAS AF= 0.0381 (184/4830). AF 95% confidence interval is 0.0336. There are 59 homozygotes in gnomad4. There are 1596 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 59 gene

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: 0.0211 AC: 3217 AN: 152218 Hom.: 59 Cov.: 32

Gnomad AFR AF: 0.00536

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0211 AC: 3218 AN: 152336 Hom.: 59 Cov.: 32 AF XY: 0.0214 AC XY: 1596 AN XY: 74482

Gnomad4 AFR AF: 0.00534

Gnomad4 AMR AF: 0.0182

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.0229

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0213

Alfa AF: 0.0215 Hom.: 7

Bravo AF: 0.0201

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.9
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75849835; hg19: chr1-221475899;