Variant rs1370041 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.606 in 151,984 control chromosomes in the GnomAD database, including 28,561 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 0.61 ( 28561 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.318

Variant links:

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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 (EAS) allele frequency at 95% confidence interval = 0.677 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:

0.606

AC:

92058

AN:

151866

Hom.:

28544

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.643

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.681

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.682

Gnomad FIN

AF:

0.658

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.664

Gnomad OTH

AF:

0.600

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

GnomAD4 genome

AF:

0.606

AC:

92122

AN:

151984

Hom.:

28561

Cov.:

AF XY:

0.611

AC XY:

45387

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.461

Gnomad4 AMR

AF:

0.634

Gnomad4 ASJ

AF:

0.681

Gnomad4 EAS

AF:

0.696

Gnomad4 SAS

AF:

0.682

Gnomad4 FIN

AF:

0.658

Gnomad4 NFE

AF:

0.664

Gnomad4 OTH

AF:

0.601

Alfa

AF:

0.628

Hom.:

5246

Bravo

AF:

0.598

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.88

DANN

Benign

0.44

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over