17-81402198-C-A

Variant names:

• chr17-81402198-C-A
• rs1701
• NM_001377448.1:c.178+2281C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377448.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAHCC1	NM_001377448.1	MANE Select	c.178+2281C>A		intron	N/A	NP_001364377.1
	BAHCC1	NM_001291324.3		c.178+2281C>A		intron	N/A	NP_001278253.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAHCC1	ENST00000675386.2	MANE Select	c.178+2281C>A		intron	N/A	ENSP00000502710.1
	BAHCC1	ENST00000625166.1	TSL:6	n.1109C>A		non_coding_transcript_exon	Exon 1 of 1
	BAHCC1	ENST00000584436.7	TSL:5	c.178+2281C>A		intron	N/A	ENSP00000462154.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 4 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 2 AN: 10

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.272 AC: 41369 AN: 152134 Hom.: 6908 Cov.: 32 AF XY: 0.270 AC XY: 20111 AN XY: 74350

African (AFR) AF: 0.116 AC: 4813 AN: 41536

American (AMR) AF: 0.216 AC: 3309 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3464

East Asian (EAS) AF: 0.00791 AC: 41 AN: 5182

South Asian (SAS) AF: 0.258 AC: 1246 AN: 4826

European-Finnish (FIN) AF: 0.390 AC: 4116 AN: 10562

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25156 AN: 67950

Other (OTH) AF: 0.293 AC: 618 AN: 2112

Alfa AF: 0.321 Hom.: 16555

Bravo AF: 0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.66
PhyloP100		0.017

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

Other links and lift over

dbSNP: rs1701; hg19: chr17-79375998;