chr3-154559627-T-G

Variant names:

• chr3-154559627-T-G
• rs6765660

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 0.23 in 152,042 control chromosomes in the GnomAD database, including 6,380 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 0.23 (6380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 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: 0.230 AC: 34891 AN: 151924 Hom.: 6342 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.230 AC: 34989 AN: 152042 Hom.: 6380 Cov.: 32 AF XY: 0.225 AC XY: 16753 AN XY: 74322

African (AFR) AF: 0.510 AC: 21142 AN: 41434

American (AMR) AF: 0.165 AC: 2525 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.0790 AC: 408 AN: 5166

South Asian (SAS) AF: 0.148 AC: 713 AN: 4830

European-Finnish (FIN) AF: 0.111 AC: 1178 AN: 10582

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.119 AC: 8068 AN: 67982

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.186 Hom.: 516

Bravo AF: 0.248

Asia WGS AF: 0.183 AC: 637 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	2.2
DANN	Benign	0.60
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6765660; hg19: chr3-154277416;