rs10197919

Variant names:

• chr2-112167396-G-A
• rs10197919
• NM_153214.3:c.406+2225G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-112167396-G-A
• chr2-112167396-G-C
• chr2-112167396-G-T

Variant summary

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

The NM_153214.3(FBLN7):​c.406+2225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,884 control chromosomes in the GnomAD database, including 8,411 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 (8411 hom., cov: 32)
• Consequence: FBLN7 NM_153214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 6 publications found

Genes affected

FBLN7 (HGNC:26740): (fibulin 7) Predicted to enable calcium ion binding activity; heparan sulfate proteoglycan binding activity; and heparin binding activity. Predicted to be involved in cell adhesion. Predicted to act upstream of or within positive regulation of biomineralization. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153214.3. 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
	FBLN7	NM_153214.3	MANE Select	c.406+2225G>A		intron	N/A	NP_694946.2
	FBLN7	NM_001128165.2		c.406+2225G>A		intron	N/A	NP_001121637.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBLN7	ENST00000331203.7	TSL:1 MANE Select	c.406+2225G>A		intron	N/A	ENSP00000331411.2
	FBLN7	ENST00000409450.7	TSL:1	c.406+2225G>A		intron	N/A	ENSP00000387000.3
	FBLN7	ENST00000409667.7	TSL:1	c.406+2225G>A		intron	N/A	ENSP00000386822.3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46862 AN: 151774 Hom.: 8411 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.309 AC: 46865 AN: 151884 Hom.: 8411 Cov.: 32 AF XY: 0.303 AC XY: 22512 AN XY: 74192

African (AFR) AF: 0.136 AC: 5643 AN: 41436

American (AMR) AF: 0.315 AC: 4816 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1346 AN: 3456

East Asian (EAS) AF: 0.190 AC: 979 AN: 5144

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4816

European-Finnish (FIN) AF: 0.316 AC: 3334 AN: 10564

Middle Eastern (MID) AF: 0.555 AC: 161 AN: 290

European-Non Finnish (NFE) AF: 0.416 AC: 28213 AN: 67878

Other (OTH) AF: 0.370 AC: 780 AN: 2108

Alfa AF: 0.384 Hom.: 17769

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-0.88
Mutation Taster		=99/1	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: rs10197919; hg19: chr2-112924973;