dbSNP rs10504672: :null (chr8-78082964-G-C) – ACMG Classification: Benign (-12 pts)

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 0.439 in 151,850 control chromosomes in the GnomAD database, including 15,851 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 0.44 ( 15851 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.136

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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 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:

0.439

AC:

66600

AN:

151732

Hom.:

15821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.629

Gnomad AMI

AF:

0.499

Gnomad AMR

AF:

0.404

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.429

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

GnomAD4 genome

AF:

0.439

AC:

66681

AN:

151850

Hom.:

15851

Cov.:

AF XY:

0.436

AC XY:

32367

AN XY:

74190

show subpopulations

Gnomad4 AFR

AF:

0.629

Gnomad4 AMR

AF:

0.404

Gnomad4 ASJ

AF:

0.399

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.458

Gnomad4 FIN

AF:

0.323

Gnomad4 NFE

AF:

0.345

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.239

Hom.:

533

Bravo

AF:

0.456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.67

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