chr15-39638339-G-A

Position:

• chr15-39638339-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152597.5(FSIP1):​c.1189-20094C>T 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 152,142 control chromosomes in the GnomAD database, including 3,055 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 (3055 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611

Genes affected

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

LOC105370785 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.1189-20094C>T		intron_variant		ENST00000350221.4	NP_689810.3
LOC105370785	XR_932156.3	n.351-2236G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.1189-20094C>T		intron_variant		1	NM_152597.5	ENSP00000280236	P1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27531 AN: 152022 Hom.: 3038 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.181 AC: 27584 AN: 152142 Hom.: 3055 Cov.: 32 AF XY: 0.185 AC XY: 13790 AN XY: 74382

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.176

Alfa AF: 0.141 Hom.: 296

Bravo AF: 0.186

Asia WGS AF: 0.264 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.14

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

Publications

LitVar

Other links and lift over

dbSNP: rs8029602; hg19: chr15-39930540;