rs16991689

Variant names:

• chr22-44221682-A-G
• rs16991689
• ENST00000624215.1:n.7831T>C

Variant summary

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

The ENST00000624215.1(ENSG00000280011):​n.7831T>C 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 0.177 in 152,264 control chromosomes in the GnomAD database, including 2,882 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 0.18 (2882 hom., cov: 34)
  • Exomes 𝑓: 0.22 (0 hom.)
• Consequence: ENSG00000280011 ENST00000624215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 1 publications found

Genes affected

ENSG00000280011 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280011	ENST00000624215.1	n.7831T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26874 AN: 152110 Hom.: 2882 Cov.: 34

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.222 AC: 8 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.150 AC XY: 3 AN XY: 20

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

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: 0.300 AC: 3 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.208 AC: 5 AN: 24

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.177 AC: 26879 AN: 152228 Hom.: 2882 Cov.: 34 AF XY: 0.179 AC XY: 13301 AN XY: 74424

African (AFR) AF: 0.0609 AC: 2530 AN: 41552

American (AMR) AF: 0.150 AC: 2291 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3468

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5170

South Asian (SAS) AF: 0.160 AC: 771 AN: 4822

European-Finnish (FIN) AF: 0.260 AC: 2759 AN: 10598

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15953 AN: 68000

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.213 Hom.: 11691

Bravo AF: 0.165

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs16991689; hg19: chr22-44617562;