chr16-67018144-T-G

Variant names:

• chr16-67018144-T-G
• rs7185839
• ENST00000804323.1:n.209-2865A>C

Variant summary

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

The ENST00000804323.1(ENSG00000304523):​n.209-2865A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,074 control chromosomes in the GnomAD database, including 6,452 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 0.21 (6452 hom., cov: 32)
• Consequence: ENSG00000304523 ENST00000804323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 11 publications found

Genes affected

ENSG00000304523 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 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
ENSG00000304523	ENST00000804323.1	n.209-2865A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31599 AN: 151956 Hom.: 6432 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0508

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.208 AC: 31679 AN: 152074 Hom.: 6452 Cov.: 32 AF XY: 0.208 AC XY: 15457 AN XY: 74372

African (AFR) AF: 0.536 AC: 22215 AN: 41432

American (AMR) AF: 0.111 AC: 1695 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0508 AC: 176 AN: 3466

East Asian (EAS) AF: 0.0471 AC: 244 AN: 5180

South Asian (SAS) AF: 0.165 AC: 795 AN: 4816

European-Finnish (FIN) AF: 0.125 AC: 1321 AN: 10592

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0700 AC: 4762 AN: 67992

Other (OTH) AF: 0.160 AC: 339 AN: 2114

Alfa AF: 0.112 Hom.: 8121

Bravo AF: 0.218

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.71
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7185839; hg19: chr16-67052047;