1-172658358-C-T

Position:

• chr1-172658358-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.488 in 151,968 control chromosomes in the GnomAD database, including 21,522 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.49 (21522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-172658358-C-T is Benign according to our data. Variant chr1-172658358-C-T is described in ClinVar as [Benign]. Clinvar id is 1165021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74089 AN: 151850 Hom.: 21468 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.488 AC: 74198 AN: 151968 Hom.: 21522 Cov.: 32 AF XY: 0.483 AC XY: 35845 AN XY: 74270

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.489

Alfa AF: 0.398 Hom.: 14481

Bravo AF: 0.507

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Autoimmune lymphoproliferative syndrome type 1 Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 19, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.10
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763110; hg19: chr1-172627498; COSMIC: COSV60680908;