rs41309790

Variant names:

• chr1-172658724-A-T
• rs41309790

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.0974 in 152,304 control chromosomes in the GnomAD database, including 1,050 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.097 (1050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.132
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 1-172658724-A-T is Benign according to our data. Variant chr1-172658724-A-T is described in ClinVar as Benign. ClinVar VariationId is 1236304.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.0975 AC: 14840 AN: 152186 Hom.: 1049 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0974 AC: 14841 AN: 152304 Hom.: 1050 Cov.: 32 AF XY: 0.0942 AC XY: 7016 AN XY: 74470

African (AFR) AF: 0.0245 AC: 1018 AN: 41568

American (AMR) AF: 0.0966 AC: 1478 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5192

South Asian (SAS) AF: 0.0984 AC: 475 AN: 4826

European-Finnish (FIN) AF: 0.0818 AC: 868 AN: 10616

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9960 AN: 68016

Other (OTH) AF: 0.114 AC: 242 AN: 2116

Alfa AF: 0.113 Hom.: 132

Bravo AF: 0.0959

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 08, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.35
PhyloP100		-0.13
PromoterAI		0.0017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs41309790; hg19: chr1-172627864;