rs16832963

Variant names:

• chr2-190811941-G-C
• rs16832963
• ENST00000676095.2:n.194+3787C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000676095.2(ENSG00000228509):​n.194+3787C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0086 in 152,264 control chromosomes in the GnomAD database, including 31 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 0.0086 (31 hom., cov: 32)
• Consequence: ENSG00000228509 ENST00000676095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0086 (1310/152264) while in subpopulation AMR AF = 0.0501 (765/15276). AF 95% confidence interval is 0.0471. There are 31 homozygotes in GnomAd4. There are 780 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 31 gene

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
ENSG00000228509	ENST00000676095.2	n.194+3787C>G		intron_variant	Intron 2 of 8
ENSG00000228509	ENST00000676152.1	n.256-3026C>G		intron_variant	Intron 3 of 4
ENSG00000228509	ENST00000772360.1	n.285+3787C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.00860 AC: 1308 AN: 152146 Hom.: 32 Cov.: 32

Gnomad AFR AF: 0.00118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00121

Gnomad OTH AF: 0.00717

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

GnomAD4 genome AF: 0.00860 AC: 1310 AN: 152264 Hom.: 31 Cov.: 32 AF XY: 0.0105 AC XY: 780 AN XY: 74458

African (AFR) AF: 0.00118 AC: 49 AN: 41552

American (AMR) AF: 0.0501 AC: 765 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.000577 AC: 2 AN: 3468

East Asian (EAS) AF: 0.0479 AC: 248 AN: 5182

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4828

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00121 AC: 82 AN: 68028

Other (OTH) AF: 0.00710 AC: 15 AN: 2114

Alfa AF: 0.00450 Hom.: 3

Bravo AF: 0.0124

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16832963; hg19: chr2-191676667;