rs2077678

Variant names:

• chr1-75069143-A-G
• rs2077678

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 0.153 in 152,130 control chromosomes in the GnomAD database, including 2,083 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 (2083 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.153 AC: 23240 AN: 152012 Hom.: 2078 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.153 AC: 23243 AN: 152130 Hom.: 2083 Cov.: 32 AF XY: 0.154 AC XY: 11464 AN XY: 74390

Gnomad4 AFR AF: 0.0622

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.154

Alfa AF: 0.166 Hom.: 347

Bravo AF: 0.146

Asia WGS AF: 0.224 AC: 775 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077678; hg19: chr1-75534827;