rs4650608

Variant names:

• chr1-78772330-T-C
• rs4650608

Your query was ambiguous. Multiple possible variants found:

• chr1-78772330-T-C
• chr1-78772330-T-G

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 0.288 in 152,090 control chromosomes in the GnomAD database, including 6,648 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 0.29 (6648 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 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: 0.288 AC: 43831 AN: 151972 Hom.: 6645 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.288 AC: 43849 AN: 152090 Hom.: 6648 Cov.: 32 AF XY: 0.287 AC XY: 21321 AN XY: 74364

African (AFR) AF: 0.257 AC: 10673 AN: 41478

American (AMR) AF: 0.285 AC: 4361 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3470

East Asian (EAS) AF: 0.0455 AC: 236 AN: 5182

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3559 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22185 AN: 67968

Other (OTH) AF: 0.260 AC: 550 AN: 2114

Alfa AF: 0.309 Hom.: 25002

Bravo AF: 0.281

Asia WGS AF: 0.159 AC: 555 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	7.2
DANN	Benign	0.54
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4650608; hg19: chr1-79238015;