chr1-15753676-G-A

Position:

• chr1-15753676-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.205 in 152,170 control chromosomes in the GnomAD database, including 3,345 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 (3345 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31270 AN: 152052 Hom.: 3343 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.205 AC: 31267 AN: 152170 Hom.: 3345 Cov.: 32 AF XY: 0.200 AC XY: 14893 AN XY: 74384

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.204

Alfa AF: 0.224 Hom.: 8285

Bravo AF: 0.204

Asia WGS AF: 0.148 AC: 514 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	0.20
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12725198; hg19: chr1-16080171;