rs2949192

Positions:

• chr7-1164205-G-A

Variant summary

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

The NR_110065.1(ZFAND2A-DT):​n.657G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,050 control chromosomes in the GnomAD database, including 33,362 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 0.66 (33359 hom., cov: 32)
  • Exomes 𝑓: 0.56 (3 hom.)
• Consequence: ZFAND2A-DT NR_110065.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

Genes affected

ZFAND2A-DT (HGNC:41187): (ZFAND2A divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFAND2A-DT	NR_110065.1	n.657G>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFAND2A-DT	ENST00000423008.2	n.339G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99688 AN: 151912 Hom.: 33318 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.614

GnomAD4 exome AF: 0.556 AC: 10 AN: 18 Hom.: 3 Cov.: 0 AF XY: 0.400 AC XY: 4 AN XY: 10

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.656 AC: 99774 AN: 152032 Hom.: 33359 Cov.: 32 AF XY: 0.653 AC XY: 48470 AN XY: 74270

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.610

Alfa AF: 0.632 Hom.: 31554

Bravo AF: 0.657

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2949192; hg19: chr7-1203841; COSMIC: COSV57180632;