Variant rs1701 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001377448.1(BAHCC1):c.178+2281C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,160 control chromosomes in the GnomAD database, including 6,909 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 ( 6908 hom., cov: 32)

Exomes 𝑓: 0.27 ( 1 hom. )

Consequence

BAHCC1
NM_001377448.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0170

Variant links:

Genes affected

BAHCC1 (HGNC:29279): (BAH domain and coiled-coil containing 1) Predicted to enable chromatin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

BAHCC1 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAHCC1	NM_001377448.1 linkuse as main transcript	c.178+2281C>A		intron_variant		ENST00000675386.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
BAHCC1	ENST00000675386.2 linkuse as main transcript	c.178+2281C>A	intron_variant			NM_001377448.1	P2
BAHCC1	ENST00000584436.7 linkuse as main transcript	c.178+2281C>A	intron_variant		5		A2
BAHCC1	ENST00000625166.1 linkuse as main transcript	n.1109C>A	non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41371

AN:

152018

Hom.:

6912

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.536

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.421

Gnomad EAS

AF:

0.00789

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.370

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.269

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.400

Gnomad4 NFE exome

AF:

0.200

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.272

AC:

41369

AN:

152134

Hom.:

6908

Cov.:

AF XY:

0.270

AC XY:

20111

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.216

Gnomad4 ASJ

AF:

0.421

Gnomad4 EAS

AF:

0.00791

Gnomad4 SAS

AF:

0.258

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.370

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.348

Hom.:

8399

Bravo

AF:

0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.6

DANN

Benign

0.66

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