rs16864170

Variant names:

• chr2-5767748-T-C
• rs16864170
• ENST00000829845.1:n.329-22808T>C

Variant summary

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

The ENST00000829845.1(ENSG00000236106):​n.329-22808T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 152,288 control chromosomes in the GnomAD database, including 170 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 0.039 (170 hom., cov: 33)
• Consequence: ENSG00000236106 ENST00000829845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 12 publications found

Genes affected

ENSG00000236106 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829845.1. 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
	ENSG00000236106	ENST00000829845.1		n.329-22808T>C		intron	N/A
	ENSG00000236106	ENST00000829846.1		n.318-22808T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5920 AN: 152170 Hom.: 172 Cov.: 33

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0389 AC: 5918 AN: 152288 Hom.: 170 Cov.: 33 AF XY: 0.0410 AC XY: 3050 AN XY: 74480

African (AFR) AF: 0.0233 AC: 967 AN: 41566

American (AMR) AF: 0.0298 AC: 456 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3466

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5178

South Asian (SAS) AF: 0.144 AC: 697 AN: 4826

European-Finnish (FIN) AF: 0.0418 AC: 443 AN: 10608

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0451 AC: 3068 AN: 68020

Other (OTH) AF: 0.0468 AC: 99 AN: 2116

Alfa AF: 0.0417 Hom.: 306

Bravo AF: 0.0339

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.73
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16864170;

hg19: chr2-5907880;