rs2949192

Variant names:

• chr7-1164205-G-A
• rs2949192
• ENST00000422230.1:n.175G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-1164205-G-A
• chr7-1164205-G-C
• chr7-1164205-G-T

Variant summary

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

The ENST00000422230.1(ZFAND2A-DT):​n.175G>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 ENST00000422230.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 20 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZFAND2A-DT	NR_110065.1	n.657G>A		non_coding_transcript_exon_variant	Exon 4 of 4
ZFAND2A-DT	NR_110066.1	n.339G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ZFAND2A-DT	NR_110067.1	n.595G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFAND2A-DT	ENST00000422230.1	n.175G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4
ZFAND2A-DT	ENST00000423008.2	n.339G>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
ZFAND2A-DT	ENST00000655003.1	n.363G>A		non_coding_transcript_exon_variant	Exon 4 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 5 AN: 10

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.763 AC: 31652 AN: 41486

American (AMR) AF: 0.608 AC: 9289 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2107 AN: 5152

South Asian (SAS) AF: 0.564 AC: 2720 AN: 4820

European-Finnish (FIN) AF: 0.642 AC: 6760 AN: 10536

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43034 AN: 67976

Other (OTH) AF: 0.610 AC: 1288 AN: 2112

Alfa AF: 0.644 Hom.: 55431

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
PhyloP100		-0.70

Splicing

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

Other links and lift over

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