chr8-140516886-G-C

Variant names:

• chr8-140516886-G-C
• rs10216653
• NM_017444.6:c.*1639G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017444.6(CHRAC1):​c.*1639G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 151,996 control chromosomes in the GnomAD database, including 49,328 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 0.80 (49327 hom., cov: 31)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: CHRAC1 NM_017444.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 8 publications found

Genes affected

CHRAC1 (HGNC:13544): (chromatin accessibility complex subunit 1) CHRAC1 is a histone-fold protein that interacts with other histone-fold proteins to bind DNA in a sequence-independent manner. These histone-fold protein dimers combine within larger enzymatic complexes for DNA transcription, replication, and packaging.[supplied by OMIM, Apr 2004]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHRAC1	NM_017444.6	c.*1639G>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000220913.10	NP_059140.1
CHRAC1	NR_023360.3	n.2086G>C		non_coding_transcript_exon_variant	Exon 2 of 2
CHRAC1	NR_040712.2	n.1918G>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHRAC1	ENST00000220913.10	c.*1639G>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_017444.6	ENSP00000220913.5

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121932 AN: 151874 Hom.: 49281 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.810

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.803 AC: 122036 AN: 151992 Hom.: 49327 Cov.: 31 AF XY: 0.798 AC XY: 59268 AN XY: 74272

African (AFR) AF: 0.738 AC: 30587 AN: 41438

American (AMR) AF: 0.830 AC: 12687 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3171 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3877 AN: 5166

South Asian (SAS) AF: 0.754 AC: 3633 AN: 4818

European-Finnish (FIN) AF: 0.728 AC: 7663 AN: 10522

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57648 AN: 67982

Other (OTH) AF: 0.814 AC: 1717 AN: 2110

Alfa AF: 0.828 Hom.: 6479

Bravo AF: 0.807

Asia WGS AF: 0.748 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.4
DANN	Benign	0.79
PhyloP100		0.76
Mutation Taster		=100/0	polymorphism (auto)

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: rs10216653; hg19: chr8-141526985;