chr8-5066615-T-C

Variant names:

• chr8-5066615-T-C
• rs2977724

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 0.152 in 152,152 control chromosomes in the GnomAD database, including 2,066 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 0.15 (2066 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.554
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 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: 0.152 AC: 23083 AN: 152034 Hom.: 2058 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00654

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.152 AC: 23127 AN: 152152 Hom.: 2066 Cov.: 33 AF XY: 0.148 AC XY: 11003 AN XY: 74400

African (AFR) AF: 0.244 AC: 10106 AN: 41502

American (AMR) AF: 0.118 AC: 1807 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3470

East Asian (EAS) AF: 0.00656 AC: 34 AN: 5186

South Asian (SAS) AF: 0.160 AC: 772 AN: 4828

European-Finnish (FIN) AF: 0.0841 AC: 891 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8524 AN: 67966

Other (OTH) AF: 0.134 AC: 283 AN: 2112

Alfa AF: 0.142 Hom.: 864

Bravo AF: 0.156

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2977724; hg19: chr8-4924137;