1-207492716-C-T

Variant names:

• chr1-207492716-C-T
• rs4618971

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 0.762 in 152,072 control chromosomes in the GnomAD database, including 44,433 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 0.76 (44433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.762 AC: 115859 AN: 151954 Hom.: 44421 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.762 AC: 115920 AN: 152072 Hom.: 44433 Cov.: 31 AF XY: 0.767 AC XY: 56988 AN XY: 74342

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.748

Alfa AF: 0.756 Hom.: 11261

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.012
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4618971; hg19: chr1-207666061;