chr16-48503510-C-T

Variant names:

• chr16-48503510-C-T
• rs1004704
• ENST00000730337.1:n.318-860C>T

Variant summary

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

The ENST00000730337.1(ENSG00000295475):​n.318-860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,164 control chromosomes in the GnomAD database, including 5,882 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 0.24 (5882 hom., cov: 33)
• Consequence: ENSG00000295475 ENST00000730337.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 12 publications found

Genes affected

ENSG00000295475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730337.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295475	ENST00000730337.1		n.318-860C>T		intron	N/A
	ENSG00000295475	ENST00000730351.1		n.323-860C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36322 AN: 152046 Hom.: 5878 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.239 AC: 36335 AN: 152164 Hom.: 5882 Cov.: 33 AF XY: 0.249 AC XY: 18544 AN XY: 74374

African (AFR) AF: 0.113 AC: 4705 AN: 41528

American (AMR) AF: 0.324 AC: 4953 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3470

East Asian (EAS) AF: 0.801 AC: 4144 AN: 5174

South Asian (SAS) AF: 0.402 AC: 1937 AN: 4818

European-Finnish (FIN) AF: 0.329 AC: 3479 AN: 10576

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15723 AN: 67992

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.241 Hom.: 15656

Bravo AF: 0.240

Asia WGS AF: 0.508 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.8
DANN	Benign	0.77
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1004704;

hg19: chr16-48537421;