rs41278794

Variant names:

• chr7-92529026-C-A
• rs41278794
• NM_032120.4:c.111+102C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-92529026-C-A
• chr7-92529026-C-G
• chr7-92529026-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032120.4(RBM48):​c.111+102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000286 in 700,150 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: RBM48 NM_032120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.823
• Publications: 0 publications found

Genes affected

RBM48 (HGNC:21785): (RNA binding motif protein 48) Predicted to enable RNA binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM48	NM_032120.4	c.111+102C>A		intron_variant	Intron 1 of 4	ENST00000265732.10	NP_115496.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM48	ENST00000265732.10	c.111+102C>A		intron_variant	Intron 1 of 4	1	NM_032120.4	ENSP00000265732.5
RBM48	ENST00000481551.5	c.111+102C>A		intron_variant	Intron 1 of 3	1		ENSP00000419242.1
RBM48	ENST00000496410.1	c.-221C>A		5_prime_UTR_variant	Exon 1 of 3	3		ENSP00000418333.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000286 AC: 2 AN: 700150 Hom.: 0 Cov.: 9 AF XY: 0.00000542 AC XY: 2 AN XY: 369218

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 17874

American (AMR) AF: 0.0000311 AC: 1 AN: 32204

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20584

East Asian (EAS) AF: 0.00 AC: 0 AN: 32416

South Asian (SAS) AF: 0.00 AC: 0 AN: 64682

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4302

European-Non Finnish (NFE) AF: 0.00000225 AC: 1 AN: 444602

Other (OTH) AF: 0.00 AC: 0 AN: 35062

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.9
DANN	Benign	0.81
PhyloP100		0.82
PromoterAI		-0.021	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs41278794; hg19: chr7-92158340;