NM_005483.3:c.961-3307C>T

Variant names:

• chr19-4414713-C-T
• rs105038
• NM_005483.3:c.961-3307C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CHAF1A	NM_005483.3	c.961-3307C>T		intron_variant	Intron 3 of 14	ENST00000301280.10	NP_005474.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHAF1A	ENST00000301280.10	c.961-3307C>T		intron_variant	Intron 3 of 14	1	NM_005483.3	ENSP00000301280.4
CHAF1A	ENST00000587739.1	c.315+4954C>T		intron_variant	Intron 1 of 4	5		ENSP00000467296.1

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

African (AFR) AF: 0.344 AC: 14245 AN: 41438

American (AMR) AF: 0.427 AC: 6507 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1150 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3076 AN: 5154

South Asian (SAS) AF: 0.372 AC: 1789 AN: 4814

European-Finnish (FIN) AF: 0.337 AC: 3552 AN: 10546

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18570 AN: 67980

Other (OTH) AF: 0.338 AC: 715 AN: 2114

Alfa AF: 0.300 Hom.: 8905

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
PhyloP100		-1.0
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: rs105038; hg19: chr19-4414710;