chr1-191193417-A-T

Variant names:

• chr1-191193417-A-T
• rs2061018

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 0.481 in 151,902 control chromosomes in the GnomAD database, including 17,685 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 0.48 (17685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 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: 0.481 AC: 73017 AN: 151786 Hom.: 17671 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.481 AC: 73085 AN: 151902 Hom.: 17685 Cov.: 31 AF XY: 0.481 AC XY: 35709 AN XY: 74212

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.472

Alfa AF: 0.367 Hom.: 988

Bravo AF: 0.485

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2061018; hg19: chr1-191162547;