1-191658617-T-A

Position:

• chr1-191658617-T-A

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 0.0603 in 152,182 control chromosomes in the GnomAD database, including 423 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 0.060 (423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0602 AC: 9160 AN: 152064 Hom.: 422 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0603 AC: 9175 AN: 152182 Hom.: 423 Cov.: 32 AF XY: 0.0609 AC XY: 4530 AN XY: 74382

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0472

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0604

Gnomad4 FIN AF: 0.0236

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0149 Hom.: 8

Bravo AF: 0.0649

Asia WGS AF: 0.0980 AC: 340 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494655; hg19: chr1-191627747;