rs2161510

Variant names:

• chr16-15217755-T-C
• rs2161510
• ENST00000737633.1:n.82+39347A>G

Variant summary

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

The ENST00000737633.1(ENSG00000296252):​n.82+39347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 146,850 control chromosomes in the GnomAD database, including 23,188 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 0.55 (23188 hom., cov: 23)
• Consequence: ENSG00000296252 ENST00000737633.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 1 publications found

Genes affected

ENSG00000296252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737633.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296252	ENST00000737633.1		n.82+39347A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 80787 AN: 146734 Hom.: 23170 Cov.: 23

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.600

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.550 AC: 80839 AN: 146850 Hom.: 23188 Cov.: 23 AF XY: 0.546 AC XY: 39010 AN XY: 71454

African (AFR) AF: 0.347 AC: 14077 AN: 40522

American (AMR) AF: 0.641 AC: 9252 AN: 14434

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2247 AN: 3328

East Asian (EAS) AF: 0.403 AC: 2000 AN: 4958

South Asian (SAS) AF: 0.421 AC: 1949 AN: 4628

European-Finnish (FIN) AF: 0.628 AC: 6304 AN: 10040

Middle Eastern (MID) AF: 0.657 AC: 180 AN: 274

European-Non Finnish (NFE) AF: 0.654 AC: 43045 AN: 65772

Other (OTH) AF: 0.595 AC: 1199 AN: 2014

Alfa AF: 0.596 Hom.: 2942

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0030
DANN	Benign	0.54
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2161510; hg19: chr16-15311612;