rs6492915

Variant names:

• chr15-39745559-T-G
• rs6492915
• NM_152597.5:c.560-3659A>C

Variant summary

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

The NM_152597.5(FSIP1):​c.560-3659A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,120 control chromosomes in the GnomAD database, including 3,844 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 0.18 (3844 hom., cov: 31)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 1 publications found

Genes affected

FSIP1 (HGNC:21674): (fibrous sheath interacting protein 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152597.5. 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
	FSIP1	NM_152597.5	MANE Select	c.560-3659A>C		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.560-3659A>C		intron	N/A	NP_001311267.1	Q8NA03

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	ENST00000350221.4	TSL:1 MANE Select	c.560-3659A>C		intron	N/A	ENSP00000280236.3	Q8NA03
	FSIP1	ENST00000884361.1		c.560-3659A>C		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.560-3659A>C		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28054 AN: 152002 Hom.: 3834 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.176

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.185 AC: 28102 AN: 152120 Hom.: 3844 Cov.: 31 AF XY: 0.193 AC XY: 14328 AN XY: 74372

African (AFR) AF: 0.305 AC: 12632 AN: 41474

American (AMR) AF: 0.309 AC: 4722 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2318 AN: 5154

South Asian (SAS) AF: 0.200 AC: 965 AN: 4824

European-Finnish (FIN) AF: 0.189 AC: 2004 AN: 10580

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0688 AC: 4679 AN: 68014

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.138 Hom.: 289

Bravo AF: 0.203

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.23
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism (auto)

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: rs6492915; hg19: chr15-40037760;