16-46474032-G-T

Variant names:

• chr16-46474032-G-T
• rs7197337
• ENST00000566201.7:n.3559+217C>A

Variant summary

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

The ENST00000566201.7(ENSG00000290429):​n.3559+217C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 215,636 control chromosomes in the GnomAD database, including 101,845 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 0.96 (70574 hom., cov: 29)
  • Exomes 𝑓: 0.99 (31271 hom.)
• Consequence: ENSG00000290429 ENST00000566201.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 3 publications found

Genes affected

ENSG00000290429 (HGNC:):

ANKRD26P1 (HGNC:32955): (ankyrin repeat domain 26 pseudogene 1)

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 (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD26P1	NR_026556.1	n.3531+217C>A		intron_variant	Intron 16 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290429	ENST00000566201.7	n.3559+217C>A		intron_variant	Intron 16 of 16	1
ENSG00000290429	ENST00000571006.5	n.2153+217C>A		intron_variant	Intron 9 of 9	1
ENSG00000290429	ENST00000566933.5	n.240+217C>A		intron_variant	Intron 2 of 2	3
ENSG00000290429	ENST00000571606.1	n.*90C>A		downstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146191 AN: 151958 Hom.: 70546 Cov.: 29

Gnomad AFR AF: 0.868

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.974

GnomAD4 exome AF: 0.991 AC: 63011 AN: 63560 Hom.: 31271 AF XY: 0.993 AC XY: 33675 AN XY: 33914

African (AFR) AF: 0.861 AC: 2763 AN: 3208

American (AMR) AF: 0.991 AC: 6565 AN: 6622

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 1435 AN: 1436

East Asian (EAS) AF: 1.00 AC: 4559 AN: 4560

South Asian (SAS) AF: 0.999 AC: 9711 AN: 9720

European-Finnish (FIN) AF: 1.00 AC: 2818 AN: 2818

Middle Eastern (MID) AF: 0.995 AC: 213 AN: 214

European-Non Finnish (NFE) AF: 0.999 AC: 31857 AN: 31876

Other (OTH) AF: 0.995 AC: 3090 AN: 3106

GnomAD4 genome AF: 0.962 AC: 146269 AN: 152076 Hom.: 70574 Cov.: 29 AF XY: 0.963 AC XY: 71575 AN XY: 74336

African (AFR) AF: 0.867 AC: 35936 AN: 41448

American (AMR) AF: 0.987 AC: 15086 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3467 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5142 AN: 5144

South Asian (SAS) AF: 1.00 AC: 4794 AN: 4796

European-Finnish (FIN) AF: 1.00 AC: 10610 AN: 10610

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67974 AN: 68004

Other (OTH) AF: 0.974 AC: 2057 AN: 2112

Alfa AF: 0.932 Hom.: 2134

Bravo AF: 0.956

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs7197337; hg19: chr16-46507944;