chr15-39638668-A-G

Variant names:

• chr15-39638668-A-G
• rs16969475
• NM_152597.5:c.1189-20423T>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.1189-20423T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,098 control chromosomes in the GnomAD database, including 3,037 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 (3037 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 3 publications found

Genes affected

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

ENSG00000294097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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.1189-20423T>C		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.1189-20423T>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.1189-20423T>C		intron	N/A	ENSP00000280236.3	Q8NA03
	FSIP1	ENST00000884361.1		c.1189-20423T>C		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.1030-20423T>C		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27501 AN: 151980 Hom.: 3020 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.181 AC: 27553 AN: 152098 Hom.: 3037 Cov.: 32 AF XY: 0.185 AC XY: 13757 AN XY: 74340

African (AFR) AF: 0.287 AC: 11874 AN: 41428

American (AMR) AF: 0.156 AC: 2392 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3468

East Asian (EAS) AF: 0.320 AC: 1658 AN: 5178

South Asian (SAS) AF: 0.179 AC: 862 AN: 4818

European-Finnish (FIN) AF: 0.197 AC: 2087 AN: 10586

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7721 AN: 68002

Other (OTH) AF: 0.177 AC: 375 AN: 2114

Alfa AF: 0.145 Hom.: 330

Bravo AF: 0.186

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.024
DANN	Benign	0.40
PhyloP100		-2.5
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: rs16969475; hg19: chr15-39930869;