rs16871226

Variant names:

• chr6-32948074-A-G
• rs16871226
• ENST00000429234.1:c.88+4875T>C

Variant summary

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

The ENST00000429234.1(ENSG00000248993):​c.88+4875T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0368 in 152,302 control chromosomes in the GnomAD database, including 136 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 0.037 (136 hom., cov: 32)
• Consequence: ENSG00000248993 ENST00000429234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 10 publications found

Genes affected

ENSG00000248993 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.063 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
ENSG00000248993	ENST00000429234.1	c.88+4875T>C		intron_variant	Intron 1 of 3	2		ENSP00000412457.1

Frequencies

GnomAD3 genomes AF: 0.0368 AC: 5606 AN: 152184 Hom.: 136 Cov.: 32

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0368 AC: 5610 AN: 152302 Hom.: 136 Cov.: 32 AF XY: 0.0352 AC XY: 2624 AN XY: 74478

African (AFR) AF: 0.0646 AC: 2685 AN: 41554

American (AMR) AF: 0.0314 AC: 481 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3466

East Asian (EAS) AF: 0.0689 AC: 357 AN: 5180

South Asian (SAS) AF: 0.0248 AC: 120 AN: 4832

European-Finnish (FIN) AF: 0.00160 AC: 17 AN: 10622

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0265 AC: 1802 AN: 68022

Other (OTH) AF: 0.0449 AC: 95 AN: 2116

Alfa AF: 0.0365 Hom.: 300

Bravo AF: 0.0424

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.70
PhyloP100		-0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs16871226; hg19: chr6-32915851;