rs79907974

Variant names:

• chr1-17304911-T-C
• rs79907974

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 0.0236 in 152,344 control chromosomes in the GnomAD database, including 95 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 0.024 (95 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 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: 0.0236 AC: 3586 AN: 152226 Hom.: 93 Cov.: 34

Gnomad AFR AF: 0.00535

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0130

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0236 AC: 3594 AN: 152344 Hom.: 95 Cov.: 34 AF XY: 0.0247 AC XY: 1841 AN XY: 74502

Gnomad4 AFR AF: 0.00534

Gnomad4 AMR AF: 0.0129

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.0429

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.0287

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0228 Hom.: 5

Bravo AF: 0.0192

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79907974; hg19: chr1-17631406;