rs1994816

Positions:

• chr4-180047278-G-A

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, non coding transcript 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: ENST00000663768.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663768.1	n.503+10263C>T		intron_variant, non_coding_transcript_variant

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;