Variant chr1-51123983-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001136508.2(C1orf185):c.258+5182G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 150,572 control chromosomes in the GnomAD database, including 37,653 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 0.68 ( 37653 hom., cov: 29)

Consequence

C1orf185
NM_001136508.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.248

Variant links:

Genes affected

C1orf185 (HGNC:28096): (chromosome 1 open reading frame 185) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

C1orf185 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=-0.95).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf185	NM_001136508.2 linkuse as main transcript	c.258+5182G>T		intron_variant		ENST00000371759.7

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
C1orf185	ENST00000371759.7 linkuse as main transcript	c.258+5182G>T	intron_variant	2	NM_001136508.2	P1
C1orf185	ENST00000467127.5 linkuse as main transcript	c.75+5182G>T	intron_variant	3
C1orf185	ENST00000648827.1 linkuse as main transcript	c.258+5182G>T	intron_variant
C1orf185	ENST00000474016.1 linkuse as main transcript	n.339+5182G>T	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.683

AC:

102806

AN:

150466

Hom.:

37666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.384

Gnomad AMI

AF:

0.884

Gnomad AMR

AF:

0.801

Gnomad ASJ

AF:

0.757

Gnomad EAS

AF:

0.754

Gnomad SAS

AF:

0.760

Gnomad FIN

AF:

0.837

Gnomad MID

AF:

0.760

Gnomad NFE

AF:

0.796

Gnomad OTH

AF:

0.720

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

GnomAD4 genome

AF:

0.683

AC:

102801

AN:

150572

Hom.:

37653

Cov.:

AF XY:

0.689

AC XY:

50675

AN XY:

73524

show subpopulations

Gnomad4 AFR

AF:

0.383

Gnomad4 AMR

AF:

0.801

Gnomad4 ASJ

AF:

0.757

Gnomad4 EAS

AF:

0.754

Gnomad4 SAS

AF:

0.759

Gnomad4 FIN

AF:

0.837

Gnomad4 NFE

AF:

0.796

Gnomad4 OTH

AF:

0.713

Alfa

AF:

0.775

Hom.:

44065

Bravo

AF:

0.670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.14

DANN

Benign

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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