16-51064516-G-C

Variant names:

• chr16-51064516-G-C
• rs1528601
• ENST00000785664.1:n.408-2104C>G

Variant summary

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

The ENST00000785664.1(ENSG00000287718):​n.408-2104C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 357,250 control chromosomes in the GnomAD database, including 20,822 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 0.36 (11277 hom., cov: 32)
  • Exomes 𝑓: 0.28 (9545 hom.)
• Consequence: ENSG00000287718 ENST00000785664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 14 publications found

Genes affected

ENSG00000287718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785664.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287718	ENST00000785664.1		n.408-2104C>G		intron	N/A
	ENSG00000287718	ENST00000785665.1		n.517-2104C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54952 AN: 151872 Hom.: 11250 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.387

GnomAD2 exomes AF: 0.320 AC: 46120 AN: 144238 AF XY: 0.323

Gnomad AFR exome AF: 0.451

Gnomad AMR exome AF: 0.390

Gnomad ASJ exome AF: 0.311

Gnomad EAS exome AF: 0.654

Gnomad FIN exome AF: 0.235

Gnomad NFE exome AF: 0.232

Gnomad OTH exome AF: 0.291

GnomAD4 exome AF: 0.280 AC: 57395 AN: 205260 Hom.: 9545 Cov.: 0 AF XY: 0.294 AC XY: 35019 AN XY: 119276

African (AFR) AF: 0.375 AC: 1447 AN: 3862

American (AMR) AF: 0.379 AC: 7728 AN: 20388

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 2373 AN: 7772

East Asian (EAS) AF: 0.612 AC: 2058 AN: 3362

South Asian (SAS) AF: 0.444 AC: 15301 AN: 34462

European-Finnish (FIN) AF: 0.224 AC: 2600 AN: 11586

Middle Eastern (MID) AF: 0.336 AC: 378 AN: 1126

European-Non Finnish (NFE) AF: 0.203 AC: 23053 AN: 113558

Other (OTH) AF: 0.269 AC: 2457 AN: 9144

GnomAD4 genome AF: 0.362 AC: 55030 AN: 151990 Hom.: 11277 Cov.: 32 AF XY: 0.368 AC XY: 27372 AN XY: 74306

African (AFR) AF: 0.493 AC: 20406 AN: 41412

American (AMR) AF: 0.406 AC: 6210 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3468

East Asian (EAS) AF: 0.711 AC: 3681 AN: 5174

South Asian (SAS) AF: 0.532 AC: 2561 AN: 4816

European-Finnish (FIN) AF: 0.270 AC: 2855 AN: 10568

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16884 AN: 67958

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.289 Hom.: 4550

Bravo AF: 0.379

Asia WGS AF: 0.622 AC: 2163 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.64
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1528601; hg19: chr16-51098427; COSMIC: COSV50192756;