rs762515527

Variant names:

• chr20-50876068-C-A
• rs762515527
• ENST00000358791.9:c.561C>A

Your query was ambiguous. Multiple possible variants found:

• chr20-50876068-C-A
• chr20-50876068-C-T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_017843.4(BCAS4):​c.561C>A​(p.Ser187Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BCAS4 NM_017843.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

BCAS4 (HGNC:14367): (breast carcinoma amplified sequence 4) Predicted to be part of BLOC-1 complex. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904929 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 20-50876068-C-A is Benign according to our data. Variant chr20-50876068-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2652397.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.06 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017843.4. 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
	BCAS4	NM_198799.4	MANE Select	c.400-418C>A		intron	N/A	NP_942094.3	A0A804CEY2
	BCAS4	NM_017843.4		c.561C>A	p.Ser187Ser	synonymous	Exon 5 of 6	NP_060313.3	Q8TDM0-1
	BCAS4	NM_001010974.2		c.355-418C>A		intron	N/A	NP_001010974.1	Q8TDM0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS4	ENST00000358791.9	TSL:1	c.561C>A	p.Ser187Ser	synonymous	Exon 5 of 6	ENSP00000351642.5	Q8TDM0-1
	BCAS4	ENST00000609336.5	TSL:1	c.471C>A	p.Ser157Ser	synonymous	Exon 5 of 6	ENSP00000477167.1	A0A0C4DGS6
	BCAS4	ENST00000371608.8	TSL:1 MANE Select	c.400-418C>A		intron	N/A	ENSP00000360669.3	A0A804CEY2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 302434 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 172252

African (AFR) AF: 0.00 AC: 0 AN: 8580

American (AMR) AF: 0.00 AC: 0 AN: 27172

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10736

East Asian (EAS) AF: 0.00 AC: 0 AN: 9190

South Asian (SAS) AF: 0.00 AC: 0 AN: 59508

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12352

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2244

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 158516

Other (OTH) AF: 0.00 AC: 0 AN: 14136

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.58
PhyloP100		-1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs762515527; hg19: chr20-49492605;