rs16850360

Variant names:

• chr4-74006728-A-G
• rs16850360
• ENST00000669992.2:n.1035-167A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669992.2(ENSG00000287037):​n.1035-167A>G variant causes a intron 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: ENSG00000287037 ENST00000669992.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 13 publications found

Genes affected

ENSG00000287037 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124900715	XR_007058140.1	n.1136-167A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287037	ENST00000669992.2	n.1035-167A>G		intron_variant	Intron 2 of 2
ENSG00000287037	ENST00000716529.1	n.311+7366A>G		intron_variant	Intron 2 of 5
ENSG00000287037	ENST00000769988.1	n.278+7366A>G		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.0102 AC: 425 AN: 41570

American (AMR) AF: 0.0964 AC: 1474 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.123 AC: 638 AN: 5186

South Asian (SAS) AF: 0.0623 AC: 301 AN: 4828

European-Finnish (FIN) AF: 0.0300 AC: 318 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3027 AN: 68020

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0480 Hom.: 390

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs16850360; hg19: chr4-74872445;