rs1528601

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-51064516-G-A
• chr16-51064516-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000785664.1(ENSG00000287718):​n.408-2104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 207,950 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000048 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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

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
	ENSG00000287718	ENST00000785664.1		n.408-2104C>T		intron	N/A
	ENSG00000287718	ENST00000785665.1		n.517-2104C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000481 AC: 1 AN: 207950 Hom.: 0 Cov.: 0 AF XY: 0.00000827 AC XY: 1 AN XY: 120852

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 3948

American (AMR) AF: 0.00 AC: 0 AN: 20672

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7932

East Asian (EAS) AF: 0.00 AC: 0 AN: 3426

South Asian (SAS) AF: 0.00 AC: 0 AN: 35110

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 11700

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1136

European-Non Finnish (NFE) AF: 0.00000871 AC: 1 AN: 114766

Other (OTH) AF: 0.00 AC: 0 AN: 9260

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.49
PhyloP100		-0.53

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: rs1528601;

hg19: chr16-51098427;