NM_178457.3:c.3738+150C>T

Variant names:

• chr20-59194907-C-T
• rs194869
• NM_178457.3:c.3738+150C>T

Variant summary

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

The NM_178457.3(ZNF831):​c.3738+150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,145,306 control chromosomes in the GnomAD database, including 27,774 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 0.26 (5460 hom., cov: 33)
  • Exomes 𝑓: 0.21 (22314 hom.)
• Consequence: ZNF831 NM_178457.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 1 publications found

Genes affected

ZNF831 (HGNC:16167): (zinc finger protein 831) Predicted to enable metal 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF831	NM_178457.3	c.3738+150C>T		intron_variant	Intron 2 of 5	ENST00000371030.4	NP_848552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF831	ENST00000371030.4	c.3738+150C>T		intron_variant	Intron 2 of 5	1	NM_178457.3	ENSP00000360069.2
ZNF831	ENST00000637017.1	c.3738+150C>T		intron_variant	Intron 4 of 7	5		ENSP00000490240.1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39406 AN: 151992 Hom.: 5458 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.261

GnomAD4 exome AF: 0.206 AC: 204174 AN: 993196 Hom.: 22314 AF XY: 0.208 AC XY: 100275 AN XY: 483146

African (AFR) AF: 0.325 AC: 7222 AN: 22204

American (AMR) AF: 0.262 AC: 3563 AN: 13588

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 3983 AN: 16024

East Asian (EAS) AF: 0.309 AC: 9552 AN: 30944

South Asian (SAS) AF: 0.245 AC: 9864 AN: 40244

European-Finnish (FIN) AF: 0.225 AC: 9210 AN: 40888

Middle Eastern (MID) AF: 0.247 AC: 718 AN: 2912

European-Non Finnish (NFE) AF: 0.192 AC: 150665 AN: 783918

Other (OTH) AF: 0.221 AC: 9397 AN: 42474

GnomAD4 genome AF: 0.259 AC: 39448 AN: 152110 Hom.: 5460 Cov.: 33 AF XY: 0.260 AC XY: 19306 AN XY: 74354

African (AFR) AF: 0.338 AC: 14048 AN: 41512

American (AMR) AF: 0.254 AC: 3890 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.359 AC: 1849 AN: 5148

South Asian (SAS) AF: 0.259 AC: 1251 AN: 4822

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10572

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14306 AN: 67990

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.219 Hom.: 5446

Bravo AF: 0.265

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.11
DANN	Benign	0.46
PhyloP100		-2.3
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: rs194869; hg19: chr20-57769962;