chr3-55102970-A-G

Variant names:

• chr3-55102970-A-G
• rs1458977

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.355 in 152,064 control chromosomes in the GnomAD database, including 9,949 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 0.35 (9949 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.355 AC: 53937 AN: 151942 Hom.: 9944 Cov.: 33

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.355 AC: 53962 AN: 152064 Hom.: 9949 Cov.: 33 AF XY: 0.359 AC XY: 26675 AN XY: 74334

African (AFR) AF: 0.340 AC: 14118 AN: 41472

American (AMR) AF: 0.305 AC: 4659 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3468

East Asian (EAS) AF: 0.632 AC: 3265 AN: 5164

South Asian (SAS) AF: 0.379 AC: 1829 AN: 4828

European-Finnish (FIN) AF: 0.404 AC: 4279 AN: 10580

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23485 AN: 67972

Other (OTH) AF: 0.334 AC: 704 AN: 2110

Alfa AF: 0.343 Hom.: 29045

Bravo AF: 0.348

Asia WGS AF: 0.491 AC: 1704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	17
DANN	Benign	0.85
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs1458977; hg19: chr3-55136997;