rs716985

chr4-18625889-T-G

Variant summary

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

The ENST00000652661.1(ENSG00000286046):n.419-3211T>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 0.0407 in 152,258 control chromosomes in the GnomAD database, including 239 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 0.041 (239 hom., cov: 33)
• Consequence: ENST00000652661.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374510	XR_001741602.2	n.91-3211T>G		intron_variant, non_coding_transcript_variant
LOC105374510	XR_001741601.2	n.823-3211T>G		intron_variant, non_coding_transcript_variant
LOC105374510	XR_925445.3	n.433-3211T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652661.1	n.419-3211T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6177 AN: 152140 Hom.: 235 Cov.: 33

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00685

Gnomad OTH AF: 0.0379

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

GnomAD4 genome AF: 0.0407 AC: 6201 AN: 152258 Hom.: 239 Cov.: 33 AF XY: 0.0439 AC XY: 3265 AN XY: 74452

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.0914

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0786

Gnomad4 FIN AF: 0.0312

Gnomad4 NFE AF: 0.00685

Gnomad4 OTH AF: 0.0403

Alfa AF: 0.0160 Hom.: 74

Bravo AF: 0.0450

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.8
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716985; hg19: chr4-18627512;