rs2977724

Variant names:

• chr8-5066615-T-C
• rs2977724

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 0.152 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0841

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.134

Alfa AF: 0.142 Hom.: 779

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2977724; hg19: chr8-4924137;