rs4932217

Variant names:

• chr15-89358801-A-C
• rs4932217
• ENST00000772988.1:n.260T>G

Your query was ambiguous. Multiple possible variants found:

• chr15-89358801-A-C
• chr15-89358801-A-G
• chr15-89358801-A-T

Variant summary

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

The ENST00000772988.1(ENSG00000300614):​n.260T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,212 control chromosomes in the GnomAD database, including 23,697 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 0.53 (23691 hom., cov: 33)
  • Exomes 𝑓: 0.36 (6 hom.)
• Consequence: ENSG00000300614 ENST00000772988.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 15 publications found

Genes affected

ENSG00000300614 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772988.1. 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
	ENSG00000300614	ENST00000772988.1		n.260T>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000300614	ENST00000772990.1		n.233T>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000279708	ENST00000624115.1	TSL:6	n.-40A>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80150 AN: 152000 Hom.: 23648 Cov.: 33

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.362 AC: 34 AN: 94 Hom.: 6 Cov.: 0 AF XY: 0.353 AC XY: 24 AN XY: 68

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 8 AN: 20

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.344 AC: 22 AN: 64

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.527 AC: 80238 AN: 152118 Hom.: 23691 Cov.: 33 AF XY: 0.528 AC XY: 39270 AN XY: 74376

African (AFR) AF: 0.806 AC: 33466 AN: 41528

American (AMR) AF: 0.427 AC: 6540 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1331 AN: 5140

South Asian (SAS) AF: 0.482 AC: 2323 AN: 4824

European-Finnish (FIN) AF: 0.459 AC: 4849 AN: 10570

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28850 AN: 67970

Other (OTH) AF: 0.487 AC: 1026 AN: 2108

Alfa AF: 0.427 Hom.: 28018

Bravo AF: 0.538

Asia WGS AF: 0.408 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.1
DANN	Benign	0.18
PhyloP100		-0.47

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: rs4932217;

hg19: chr15-89902032;