rs763110

Variant names:

• chr1-172658358-C-T
• rs763110

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

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Autoimmune lymphoproliferative syndrome type 1 Benign:1

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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;