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).

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
ENSG00000287718	ENST00000785664.1	n.408-2104C>T		intron_variant	Intron 2 of 2
ENSG00000287718	ENST00000785665.1	n.517-2104C>T		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1528601; hg19: chr16-51098427;