rs1994816

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

ENSG00000287083 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663768.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287083	ENST00000663768.1		n.503+10263C>T		intron	N/A
	ENSG00000287083	ENST00000826563.1		n.146+11622C>T		intron	N/A
	ENSG00000287083	ENST00000826564.1		n.255+12275C>T		intron	N/A

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

African (AFR) AF: 0.473 AC: 19580 AN: 41406

American (AMR) AF: 0.305 AC: 4658 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1662 AN: 5156

South Asian (SAS) AF: 0.337 AC: 1622 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1814 AN: 10554

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10045 AN: 67976

Other (OTH) AF: 0.264 AC: 555 AN: 2100

Alfa AF: 0.188 Hom.: 15378

Bravo AF: 0.287

Asia WGS AF: 0.352 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.75
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs1994816; hg19: chr4-180968431;