rs7179742

Variant names:

• chr15-39770852-A-G
• rs7179742
• NM_152597.5:c.127-242T>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.127-242T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,108 control chromosomes in the GnomAD database, including 15,069 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 0.43 (15069 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 3 publications found

Genes affected

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

ENSG00000259580 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.493 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.127-242T>C		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.127-242T>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.127-242T>C		intron	N/A	ENSP00000280236.3	Q8NA03
	FSIP1	ENST00000884361.1		c.127-242T>C		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.127-242T>C		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66095 AN: 151990 Hom.: 15061 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.435 AC: 66136 AN: 152108 Hom.: 15069 Cov.: 32 AF XY: 0.435 AC XY: 32349 AN XY: 74354

African (AFR) AF: 0.338 AC: 14031 AN: 41514

American (AMR) AF: 0.503 AC: 7688 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1199 AN: 5162

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4822

European-Finnish (FIN) AF: 0.543 AC: 5739 AN: 10576

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33127 AN: 67958

Other (OTH) AF: 0.429 AC: 905 AN: 2112

Alfa AF: 0.464 Hom.: 46533

Bravo AF: 0.430

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.18
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7179742;

hg19: chr15-40063053;