chr2-16534140-A-G

Variant names:

• chr2-16534140-A-G
• rs4441471
• ENST00000648675.1:n.744-4242A>G

Variant summary

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

The ENST00000648675.1(ENSG00000237633):​n.744-4242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,936 control chromosomes in the GnomAD database, including 14,411 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 0.41 (14411 hom., cov: 32)
• Consequence: ENSG00000237633 ENST00000648675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 10 publications found

Genes affected

ENSG00000237633 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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
ENSG00000237633	ENST00000648675.1	n.744-4242A>G		intron_variant	Intron 3 of 6
ENSG00000237633	ENST00000667231.1	n.392-4242A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61870 AN: 151818 Hom.: 14398 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.408 AC: 61929 AN: 151936 Hom.: 14411 Cov.: 32 AF XY: 0.410 AC XY: 30472 AN XY: 74256

African (AFR) AF: 0.600 AC: 24849 AN: 41384

American (AMR) AF: 0.451 AC: 6887 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 785 AN: 3464

East Asian (EAS) AF: 0.723 AC: 3735 AN: 5164

South Asian (SAS) AF: 0.348 AC: 1681 AN: 4824

European-Finnish (FIN) AF: 0.314 AC: 3319 AN: 10560

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19561 AN: 67962

Other (OTH) AF: 0.376 AC: 792 AN: 2108

Alfa AF: 0.334 Hom.: 18518

Bravo AF: 0.431

Asia WGS AF: 0.539 AC: 1871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.74
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs4441471; hg19: chr2-16715408;