rs16850408

Variant names:

• chr4-74067090-C-A
• rs16850408
• ENST00000716529.1:n.547+6914C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-74067090-C-A
• chr4-74067090-C-G

Variant summary

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

The ENST00000716529.1(ENSG00000287037):​n.547+6914C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,764 control chromosomes in the GnomAD database, including 7,083 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 0.28 (7083 hom., cov: 32)
• Consequence: ENSG00000287037 ENST00000716529.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287037	ENST00000716529.1	n.547+6914C>A		intron_variant	Intron 4 of 5
ENSG00000287037	ENST00000716530.1	n.453+6914C>A		intron_variant	Intron 3 of 4
ENSG00000287037	ENST00000769989.1	n.509+6914C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41979 AN: 151646 Hom.: 7080 Cov.: 32

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.277 AC: 41985 AN: 151764 Hom.: 7083 Cov.: 32 AF XY: 0.277 AC XY: 20500 AN XY: 74140

African (AFR) AF: 0.0768 AC: 3183 AN: 41452

American (AMR) AF: 0.261 AC: 3971 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1257 AN: 3462

East Asian (EAS) AF: 0.446 AC: 2289 AN: 5132

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4818

European-Finnish (FIN) AF: 0.329 AC: 3459 AN: 10504

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25448 AN: 67866

Other (OTH) AF: 0.300 AC: 632 AN: 2110

Alfa AF: 0.321 Hom.: 2490

Bravo AF: 0.263

Asia WGS AF: 0.364 AC: 1263 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.21
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs16850408; hg19: chr4-74932807;