rs149970

Variant names:

• chr6-28012442-G-A
• rs149970

Your query was ambiguous. Multiple possible variants found:

• chr6-28012442-G-A
• chr6-28012442-G-T

Variant summary

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

The variant allele was found at a frequency of 0.243 in 488,550 control chromosomes in the GnomAD database, including 15,710 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 0.27 (6195 hom., cov: 32)
  • Exomes 𝑓: 0.23 (9515 hom.)
• Consequence: IQCB2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849
• Publications: 19 publications found

Genes affected

IQCB2P (HGNC:17727): (IQ motif containing B2 pseudogene)

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQCB2P		n.28012442G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN16-AS1	ENST00000716089.1	n.224-3434C>T		intron_variant	Intron 2 of 2
ZSCAN16-AS1	ENST00000716090.1	n.311-3434C>T		intron_variant	Intron 3 of 3
ZSCAN16-AS1	ENST00000733323.1	n.223-3434C>T		intron_variant	Intron 2 of 2
IQCB2P	ENST00000401788.2	n.*87G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41227 AN: 151902 Hom.: 6172 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.230 AC: 77368 AN: 336528 Hom.: 9515 AF XY: 0.229 AC XY: 41022 AN XY: 179218

African (AFR) AF: 0.397 AC: 3887 AN: 9796

American (AMR) AF: 0.259 AC: 4351 AN: 16818

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 1940 AN: 10192

East Asian (EAS) AF: 0.245 AC: 4957 AN: 20192

South Asian (SAS) AF: 0.234 AC: 9240 AN: 39442

European-Finnish (FIN) AF: 0.169 AC: 3380 AN: 19980

Middle Eastern (MID) AF: 0.174 AC: 330 AN: 1898

European-Non Finnish (NFE) AF: 0.225 AC: 44879 AN: 199028

Other (OTH) AF: 0.230 AC: 4404 AN: 19182

GnomAD4 genome AF: 0.272 AC: 41302 AN: 152022 Hom.: 6195 Cov.: 32 AF XY: 0.265 AC XY: 19724 AN XY: 74328

African (AFR) AF: 0.393 AC: 16259 AN: 41418

American (AMR) AF: 0.274 AC: 4193 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1054 AN: 5178

South Asian (SAS) AF: 0.233 AC: 1122 AN: 4820

European-Finnish (FIN) AF: 0.160 AC: 1695 AN: 10570

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15394 AN: 67962

Other (OTH) AF: 0.257 AC: 542 AN: 2110

Alfa AF: 0.272 Hom.: 1476

Bravo AF: 0.285

Asia WGS AF: 0.229 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.70
DANN	Benign	0.68
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs149970; hg19: chr6-27980220;