8-54501764-T-G

Variant names:

• chr8-54501764-T-G
• rs1072737

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 0.357 in 151,974 control chromosomes in the GnomAD database, including 10,101 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 0.36 (10101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 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: 0.357 AC: 54203 AN: 151856 Hom.: 10097 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.357 AC: 54223 AN: 151974 Hom.: 10101 Cov.: 32 AF XY: 0.354 AC XY: 26285 AN XY: 74268

African (AFR) AF: 0.256 AC: 10629 AN: 41470

American (AMR) AF: 0.361 AC: 5510 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3472

East Asian (EAS) AF: 0.185 AC: 958 AN: 5168

South Asian (SAS) AF: 0.355 AC: 1709 AN: 4820

European-Finnish (FIN) AF: 0.372 AC: 3918 AN: 10546

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28384 AN: 67936

Other (OTH) AF: 0.364 AC: 770 AN: 2114

Alfa AF: 0.394 Hom.: 6767

Bravo AF: 0.355

Asia WGS AF: 0.236 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.81
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1072737; hg19: chr8-55414324;