rs922948

Variant names:

• chr3-69393486-G-A
• rs922948
• ENST00000459638.5:c.-1+39148C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-69393486-G-A
• chr3-69393486-G-C
• chr3-69393486-G-T

Variant summary

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

The ENST00000497880.5(FRMD4B):​c.-1+39148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,066 control chromosomes in the GnomAD database, including 34,669 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 0.67 (34669 hom., cov: 31)
• Consequence: FRMD4B ENST00000497880.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 14 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497880.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMD4B	ENST00000459638.5	TSL:5	c.-1+39148C>T		intron	N/A	ENSP00000417550.1	C9JA15
	FRMD4B	ENST00000497880.5	TSL:4	c.-1+39148C>T		intron	N/A	ENSP00000417765.1	C9J7M5
	FRMD4B	ENST00000497757.1	TSL:5	n.271+39148C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102403 AN: 151946 Hom.: 34630 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.674 AC: 102500 AN: 152066 Hom.: 34669 Cov.: 31 AF XY: 0.675 AC XY: 50193 AN XY: 74336

African (AFR) AF: 0.652 AC: 27018 AN: 41456

American (AMR) AF: 0.665 AC: 10171 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2627 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3610 AN: 5166

South Asian (SAS) AF: 0.648 AC: 3128 AN: 4824

European-Finnish (FIN) AF: 0.702 AC: 7424 AN: 10576

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46205 AN: 67970

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.681 Hom.: 71207

Bravo AF: 0.672

Asia WGS AF: 0.653 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.26
PhyloP100		-0.78

Splicing

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: rs922948;

hg19: chr3-69442637;