rs6806528

Variant names:

• chr3-69203748-C-T
• rs6806528
• NM_015123.3:c.877-4974G>A

Variant summary

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

The NM_015123.3(FRMD4B):​c.877-4974G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 152,224 control chromosomes in the GnomAD database, including 567 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 0.086 (567 hom., cov: 32)
• Consequence: FRMD4B NM_015123.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 23 publications found

Genes affected

FRMD4B (HGNC:24886): (FERM domain containing 4B) This gene encodes a GRP1-binding protein which contains a FERM protein interaction domain as well as two coiled coil domains. This protein may play a role as a scaffolding protein. [provided by RefSeq, Mar 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015123.3. 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
	FRMD4B	NM_015123.3	MANE Select	c.877-4974G>A		intron	N/A	NP_055938.2	Q9Y2L6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD4B	ENST00000398540.8	TSL:1 MANE Select	c.877-4974G>A		intron	N/A	ENSP00000381549.3	Q9Y2L6-1
	FRMD4B	ENST00000863518.1		c.877-4974G>A		intron	N/A	ENSP00000533577.1
	FRMD4B	ENST00000470070.6	TSL:5	n.771-4974G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0856 AC: 13020 AN: 152106 Hom.: 566 Cov.: 32

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0680

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0856 AC: 13032 AN: 152224 Hom.: 567 Cov.: 32 AF XY: 0.0831 AC XY: 6182 AN XY: 74414

African (AFR) AF: 0.0957 AC: 3976 AN: 41534

American (AMR) AF: 0.0679 AC: 1037 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.0127 AC: 66 AN: 5188

South Asian (SAS) AF: 0.0317 AC: 153 AN: 4820

European-Finnish (FIN) AF: 0.0748 AC: 792 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6493 AN: 68024

Other (OTH) AF: 0.0840 AC: 177 AN: 2108

Alfa AF: 0.0912 Hom.: 2835

Bravo AF: 0.0859

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.80
DANN	Benign	0.67
PhyloP100		-1.2
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: rs6806528; hg19: chr3-69252899;