chr15-39740548-C-T

Variant names:

• chr15-39740548-C-T
• rs1906164
• NM_152597.5:c.656-759G>A

Variant summary

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

The NM_152597.5(FSIP1):​c.656-759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,922 control chromosomes in the GnomAD database, including 20,773 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 0.51 (20773 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	NM_152597.5	MANE Select	c.656-759G>A		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.656-759G>A		intron	N/A	NP_001311267.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	ENST00000350221.4	TSL:1 MANE Select	c.656-759G>A		intron	N/A	ENSP00000280236.3
	FSIP1	ENST00000884361.1		c.656-759G>A		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.656-759G>A		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77870 AN: 151806 Hom.: 20756 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.513 AC: 77927 AN: 151922 Hom.: 20773 Cov.: 32 AF XY: 0.505 AC XY: 37458 AN XY: 74218

African (AFR) AF: 0.649 AC: 26879 AN: 41434

American (AMR) AF: 0.399 AC: 6083 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1438 AN: 5172

South Asian (SAS) AF: 0.333 AC: 1608 AN: 4826

European-Finnish (FIN) AF: 0.480 AC: 5048 AN: 10518

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33782 AN: 67936

Other (OTH) AF: 0.492 AC: 1040 AN: 2112

Alfa AF: 0.516 Hom.: 5380

Bravo AF: 0.514

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.32
PhyloP100		-0.45
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: rs1906164; hg19: chr15-40032749;