6-33883396-G-A

Variant names:

• chr6-33883396-G-A
• rs16869652
• ENST00000603883.1:n.227G>A

Variant summary

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

The ENST00000603883.1(ANKRD36P2):​n.227G>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 0.0896 in 523,776 control chromosomes in the GnomAD database, including 2,477 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 0.11 (1063 hom., cov: 32)
  • Exomes 𝑓: 0.081 (1414 hom.)
• Consequence: ANKRD36P2 ENST00000603883.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 10 publications found

Genes affected

ANKRD36P2 (HGNC:56921):

LINC01016 (HGNC:48991): (long intergenic non-protein coding RNA 1016)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603883.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD36P2	ENST00000603883.1	TSL:6	n.227G>A		non_coding_transcript_exon	Exon 1 of 1
	LINC01016	ENST00000525912.2	TSL:3	n.698+10183C>T		intron	N/A
	LINC01016	ENST00000656906.2		n.349+9300C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16712 AN: 152048 Hom.: 1061 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0812 AC: 30191 AN: 371608 Hom.: 1414 Cov.: 0 AF XY: 0.0812 AC XY: 16705 AN XY: 205632

African (AFR) AF: 0.168 AC: 1669 AN: 9934

American (AMR) AF: 0.0684 AC: 1737 AN: 25392

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 1595 AN: 12898

East Asian (EAS) AF: 0.0434 AC: 645 AN: 14854

South Asian (SAS) AF: 0.0695 AC: 3975 AN: 57178

European-Finnish (FIN) AF: 0.0641 AC: 1972 AN: 30786

Middle Eastern (MID) AF: 0.0822 AC: 139 AN: 1690

European-Non Finnish (NFE) AF: 0.0846 AC: 16952 AN: 200346

Other (OTH) AF: 0.0813 AC: 1507 AN: 18530

GnomAD4 genome AF: 0.110 AC: 16724 AN: 152168 Hom.: 1063 Cov.: 32 AF XY: 0.107 AC XY: 7994 AN XY: 74390

African (AFR) AF: 0.172 AC: 7119 AN: 41498

American (AMR) AF: 0.0935 AC: 1429 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3472

East Asian (EAS) AF: 0.0470 AC: 244 AN: 5194

South Asian (SAS) AF: 0.0745 AC: 359 AN: 4822

European-Finnish (FIN) AF: 0.0590 AC: 624 AN: 10584

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0902 AC: 6130 AN: 67990

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.0965 Hom.: 1902

Bravo AF: 0.113

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.52
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs16869652; hg19: chr6-33851173;