4-143691747-T-A

Variant names:

• chr4-143691747-T-A
• rs6537170
• NM_001168235.2:c.5275+1366A>T

Variant summary

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

The NM_001168235.2(FREM3):​c.5275+1366A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,148 control chromosomes in the GnomAD database, including 7,395 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 0.31 (7395 hom., cov: 33)
• Consequence: FREM3 NM_001168235.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• Publications: 7 publications found

Genes affected

FREM3 (HGNC:25172): (FRAS1 related extracellular matrix 3) This gene encodes an integral membrane protein containing numerous CSPG (chondroitin sulfate proteoglycan element) repeats and Calx-beta domains. The protein belongs to the family of FRAS1/FREM extracellular matrix proteins and may play a role cell adhesion. [provided by RefSeq, Feb 2017]

GUSBP5 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FREM3	NM_001168235.2	c.5275+1366A>T		intron_variant	Intron 2 of 7	ENST00000329798.5	NP_001161707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FREM3	ENST00000329798.5	c.5275+1366A>T		intron_variant	Intron 2 of 7	5	NM_001168235.2	ENSP00000332886.5

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46547 AN: 152030 Hom.: 7378 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.306 AC: 46598 AN: 152148 Hom.: 7395 Cov.: 33 AF XY: 0.306 AC XY: 22754 AN XY: 74382

African (AFR) AF: 0.290 AC: 12033 AN: 41506

American (AMR) AF: 0.340 AC: 5202 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3468

East Asian (EAS) AF: 0.0523 AC: 271 AN: 5184

South Asian (SAS) AF: 0.340 AC: 1641 AN: 4828

European-Finnish (FIN) AF: 0.331 AC: 3501 AN: 10582

Middle Eastern (MID) AF: 0.359 AC: 104 AN: 290

European-Non Finnish (NFE) AF: 0.320 AC: 21770 AN: 67988

Other (OTH) AF: 0.313 AC: 659 AN: 2108

Alfa AF: 0.178 Hom.: 361

Bravo AF: 0.304

Asia WGS AF: 0.218 AC: 759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		0.53
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: rs6537170; hg19: chr4-144612900;