Variant 12-124867226-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000535005.5(SCARB1):n.293-89G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,172 control chromosomes in the GnomAD database, including 6,443 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 0.27 ( 6442 hom., cov: 33)

Exomes 𝑓: 0.38 ( 1 hom. )

Consequence

SCARB1
ENST00000535005.5 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.02

Variant links:

Genes affected

SCARB1 (HGNC:1664): (scavenger receptor class B member 1) The protein encoded by this gene is a plasma membrane receptor for high density lipoprotein cholesterol (HDL). The encoded protein mediates cholesterol transfer to and from HDL. In addition, this protein is a receptor for hepatitis C virus glycoprotein E2 and facilitates cell entry by the virus, SARS-CoV2. [provided by RefSeq, Oct 2021]

SCARB1 links:

LOC105370050 (HGNC:):

LOC105370050 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370050	XR_945488.3 linkuse as main transcript	n.1622+550C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARB1	ENST00000535005.5 linkuse as main transcript	n.293-89G>A		intron_variant, non_coding_transcript_variant		1
SCARB1	ENST00000541661.5 linkuse as main transcript	n.167+15276G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40909

AN:

152038

Hom.:

6440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.305

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.375

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.269

AC:

40917

AN:

152156

Hom.:

6442

Cov.:

AF XY:

0.271

AC XY:

20123

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.0999

Gnomad4 AMR

AF:

0.324

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.273

Gnomad4 FIN

AF:

0.343

Gnomad4 NFE

AF:

0.348

Gnomad4 OTH

AF:

0.306

Alfa

AF:

0.302

Hom.:

4154

Bravo

AF:

0.257

Asia WGS

AF:

0.284

AC:

986

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

Cadd

Benign

0.029

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