10-45652878-T-C

Variant names:

• chr10-45652878-T-C
• rs7091141
• NM_174890.4:c.260+106A>G

Variant summary

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

The NM_174890.4(ZFAND4):​c.260+106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 815,894 control chromosomes in the GnomAD database, including 10,127 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 0.11 (1412 hom., cov: 32)
  • Exomes 𝑓: 0.15 (8715 hom.)
• Consequence: ZFAND4 NM_174890.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 15 publications found

Genes affected

ZFAND4 (HGNC:23504): (zinc finger AN1-type containing 4) Predicted to enable zinc ion 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFAND4	NM_174890.4	c.260+106A>G		intron_variant	Intron 3 of 9	ENST00000344646.10	NP_777550.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFAND4	ENST00000344646.10	c.260+106A>G		intron_variant	Intron 3 of 9	1	NM_174890.4	ENSP00000339484.5

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17381 AN: 152112 Hom.: 1412 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.109

GnomAD4 exome AF: 0.152 AC: 101105 AN: 663664 Hom.: 8715 AF XY: 0.151 AC XY: 52236 AN XY: 345662

African (AFR) AF: 0.0276 AC: 455 AN: 16464

American (AMR) AF: 0.126 AC: 2981 AN: 23674

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 1803 AN: 15898

East Asian (EAS) AF: 0.000297 AC: 10 AN: 33630

South Asian (SAS) AF: 0.0967 AC: 4894 AN: 50632

European-Finnish (FIN) AF: 0.128 AC: 5335 AN: 41838

Middle Eastern (MID) AF: 0.0998 AC: 399 AN: 3996

European-Non Finnish (NFE) AF: 0.181 AC: 80544 AN: 444450

Other (OTH) AF: 0.142 AC: 4684 AN: 33082

GnomAD4 genome AF: 0.114 AC: 17383 AN: 152230 Hom.: 1412 Cov.: 32 AF XY: 0.108 AC XY: 8062 AN XY: 74430

African (AFR) AF: 0.0315 AC: 1311 AN: 41562

American (AMR) AF: 0.124 AC: 1891 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3466

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5184

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4822

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11757 AN: 67972

Other (OTH) AF: 0.108 AC: 228 AN: 2114

Alfa AF: 0.150 Hom.: 2070

Bravo AF: 0.112

Asia WGS AF: 0.0430 AC: 150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.16
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: rs7091141; hg19: chr10-46148326;