rs1701

chr17-81402198-C-Achr17-81402198-C-Gchr17-81402198-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

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]

ACMG classification

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	c.178+2281C>A		intron_variant		ENST00000675386.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41371 AN: 152018 Hom.: 6912 Cov.: 32

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: 7 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 5 AN XY: 20

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.: 32 AF XY: 0.270 AC XY: 20111 AN XY: 74350

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

Other links and lift over

dbSNP: rs1701; hg19: chr17-79375998;