rs2077678

Variant names:

• chr1-75069143-A-G
• rs2077678

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 0.153 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
• Publications: 2 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 (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

African (AFR) AF: 0.0622 AC: 2582 AN: 41544

American (AMR) AF: 0.179 AC: 2738 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3472

East Asian (EAS) AF: 0.149 AC: 770 AN: 5160

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10572

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12889 AN: 67966

Other (OTH) AF: 0.154 AC: 326 AN: 2112

Alfa AF: 0.163 Hom.: 348

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2077678; hg19: chr1-75534827;