rs4441471

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000237633 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.376

Alfa AF: 0.310 Hom.: 4340

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4441471; hg19: chr2-16715408;