rs4441471

chr2-16534140-A-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, non coding transcript 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: ENST00000648675.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648675.1	n.744-4242A>G		intron_variant, non_coding_transcript_variant
	ENST00000667231.1	n.392-4242A>G		intron_variant, non_coding_transcript_variant

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;