rs16909981

Variant names:

• chr9-95550750-G-C
• rs16909981
• ENST00000810379.1:n.247+2186C>G

Variant summary

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

The ENST00000810379.1(ENSG00000305315):​n.247+2186C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,198 control chromosomes in the GnomAD database, including 3,990 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 0.19 (3990 hom., cov: 33)
• Consequence: ENSG00000305315 ENST00000810379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 4 publications found

Genes affected

ENSG00000305315 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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
ENSG00000305315	ENST00000810379.1	n.247+2186C>G		intron_variant	Intron 1 of 2
ENSG00000305315	ENST00000810380.1	n.243-645C>G		intron_variant	Intron 1 of 2
ENSG00000305334	ENST00000810486.1	n.221+6G>C		splice_region_variant, intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29517 AN: 152080 Hom.: 3958 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.194 AC: 29598 AN: 152198 Hom.: 3990 Cov.: 33 AF XY: 0.191 AC XY: 14192 AN XY: 74420

African (AFR) AF: 0.379 AC: 15712 AN: 41506

American (AMR) AF: 0.114 AC: 1748 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0888 AC: 308 AN: 3468

East Asian (EAS) AF: 0.189 AC: 979 AN: 5172

South Asian (SAS) AF: 0.0949 AC: 458 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1279 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8629 AN: 68016

Other (OTH) AF: 0.178 AC: 375 AN: 2108

Alfa AF: 0.180 Hom.: 381

Bravo AF: 0.203

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.028
DANN	Benign	0.47
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs16909981; hg19: chr9-98313032;