rs105038

chr19-4414713-C-T

Variant summary

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

The NM_005483.3(CHAF1A):c.961-3307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,968 control chromosomes in the GnomAD database, including 8,740 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 0.33 (8740 hom., cov: 32)
• Consequence: CHAF1A NM_005483.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

CHAF1A (HGNC:1910): (chromatin assembly factor 1 subunit A) Chromatin assembly factor I (CAF1) is a nuclear complex consisting of p50, p60 (CHAF1B; MIM 601245), and p150 (CHAF1A) subunits that assembles histone octamers onto replicating DNA in vitro (Kaufman et al., 1995 [PubMed 7600578]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHAF1A	NM_005483.3	c.961-3307C>T		intron_variant		ENST00000301280.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHAF1A	ENST00000301280.10	c.961-3307C>T		intron_variant		1	NM_005483.3	P1
CHAF1A	ENST00000587739.1	c.315+4954C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50043 AN: 151850 Hom.: 8727 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.330 AC: 50085 AN: 151968 Hom.: 8740 Cov.: 32 AF XY: 0.336 AC XY: 24928 AN XY: 74258

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.338

Alfa AF: 0.296 Hom.: 6588

Bravo AF: 0.339

Asia WGS AF: 0.463 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.22
Dann	Benign	0.39

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: rs105038; hg19: chr19-4414710;