rs16850360

chr4-74006728-A-G

Variant summary

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

The ENST00000669992.1(ENSG00000287037):n.1035-167A>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 0.0437 in 152,294 control chromosomes in the GnomAD database, including 232 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 0.044 (232 hom., cov: 32)
• Consequence: ENST00000669992.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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
LOC124900715	XR_007058140.1	n.1136-167A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669992.1	n.1035-167A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6656 AN: 152176 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0437 AC: 6649 AN: 152294 Hom.: 232 Cov.: 32 AF XY: 0.0447 AC XY: 3331 AN XY: 74462

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.0964

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0623

Gnomad4 FIN AF: 0.0300

Gnomad4 NFE AF: 0.0445

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0444 Hom.: 77

Bravo AF: 0.0507

Asia WGS AF: 0.0930 AC: 322 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16850360; hg19: chr4-74872445;