rs2955005

Variant names:

• chr8-81706019-A-C
• rs2955005
• NM_024699.3:c.481-2895T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-81706019-A-C
• chr8-81706019-A-G
• chr8-81706019-A-T

Variant summary

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

The NM_024699.3(ZFAND1):​c.481-2895T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,088 control chromosomes in the GnomAD database, including 8,087 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 0.31 (8087 hom., cov: 32)
• Consequence: ZFAND1 NM_024699.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 12 publications found

Genes affected

ZFAND1 (HGNC:25858): (zinc finger AN1-type containing 1) Enables proteasome binding activity. Involved in cellular response to arsenite ion; positive regulation of intracellular protein transport; and stress granule disassembly. Located in cytoplasmic stress granule. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024699.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAND1	NM_024699.3	MANE Select	c.481-2895T>G		intron	N/A	NP_078975.2	Q8TCF1-1
	ZFAND1	NM_001170796.1		c.481-2916T>G		intron	N/A	NP_001164267.1	Q8TCF1-3
	ZFAND1	NM_001170797.2		c.481-2895T>G		intron	N/A	NP_001164268.1	Q8TCF1-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAND1	ENST00000220669.10	TSL:1 MANE Select	c.481-2895T>G		intron	N/A	ENSP00000220669.5	Q8TCF1-1
	ZFAND1	ENST00000523096.5	TSL:1	c.481-2916T>G		intron	N/A	ENSP00000430736.1	Q8TCF1-3
	ZFAND1	ENST00000522520.5	TSL:1	c.160-2895T>G		intron	N/A	ENSP00000429999.1	Q8TCF1-2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47351 AN: 151970 Hom.: 8081 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.312 AC: 47387 AN: 152088 Hom.: 8087 Cov.: 32 AF XY: 0.313 AC XY: 23278 AN XY: 74352

African (AFR) AF: 0.343 AC: 14219 AN: 41462

American (AMR) AF: 0.287 AC: 4389 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3466

East Asian (EAS) AF: 0.802 AC: 4152 AN: 5178

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 3001 AN: 10574

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18092 AN: 67990

Other (OTH) AF: 0.288 AC: 609 AN: 2112

Alfa AF: 0.278 Hom.: 3175

Bravo AF: 0.321

Asia WGS AF: 0.516 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		-0.41
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: rs2955005; hg19: chr8-82618254;