16-65685428-A-G

Variant names:

• chr16-65685428-A-G
• rs2045925
• ENST00000755064.1:n.132-11076T>C

Variant summary

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

The ENST00000755064.1(ENSG00000298355):​n.132-11076T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.977 in 152,318 control chromosomes in the GnomAD database, including 72,780 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 0.98 (72780 hom., cov: 31)
• Consequence: ENSG00000298355 ENST00000755064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 1 publications found

Genes affected

ENSG00000298355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 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
ENSG00000298355	ENST00000755064.1	n.132-11076T>C		intron_variant	Intron 1 of 1
ENSG00000298355	ENST00000755065.1	n.87-6431T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.977 AC: 148759 AN: 152200 Hom.: 72717 Cov.: 31

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.983

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.979

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

GnomAD4 genome AF: 0.977 AC: 148882 AN: 152318 Hom.: 72780 Cov.: 31 AF XY: 0.979 AC XY: 72940 AN XY: 74486

African (AFR) AF: 0.993 AC: 41297 AN: 41570

American (AMR) AF: 0.984 AC: 15050 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3421 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5180

South Asian (SAS) AF: 0.991 AC: 4780 AN: 4824

European-Finnish (FIN) AF: 0.983 AC: 10433 AN: 10614

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65485 AN: 68034

Other (OTH) AF: 0.979 AC: 2071 AN: 2116

Alfa AF: 0.969 Hom.: 10251

Bravo AF: 0.978

Asia WGS AF: 0.993 AC: 3454 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	0.77
DANN	Benign	0.70
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2045925; hg19: chr16-65719331;