1-197013024-C-T

Variant names:

• chr1-197013024-C-T
• rs7555070

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 0.577 in 151,920 control chromosomes in the GnomAD database, including 27,727 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 0.58 (27727 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.577 AC: 87546 AN: 151802 Hom.: 27710 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.577 AC: 87589 AN: 151920 Hom.: 27727 Cov.: 31 AF XY: 0.582 AC XY: 43264 AN XY: 74282

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.591

Alfa AF: 0.630 Hom.: 12535

Bravo AF: 0.564

Asia WGS AF: 0.747 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7555070; hg19: chr1-196982154;