rs1994816

Variant names:

• chr4-180047278-G-A
• rs1994816
• ENST00000663768.1:n.503+10263C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663768.1(ENSG00000287083):​n.503+10263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,944 control chromosomes in the GnomAD database, including 7,145 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 0.27 (7145 hom., cov: 32)
• Consequence: ENSG00000287083 ENST00000663768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

Genes affected

ENSG00000287083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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
ENSG00000287083	ENST00000663768.1	n.503+10263C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40818 AN: 151826 Hom.: 7122 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.269 AC: 40888 AN: 151944 Hom.: 7145 Cov.: 32 AF XY: 0.274 AC XY: 20352 AN XY: 74274

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.264

Alfa AF: 0.175 Hom.: 5785

Bravo AF: 0.287

Asia WGS AF: 0.352 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1994816; hg19: chr4-180968431;