NM_001378107.1:c.1624-394T>C

Variant names:

• chr2-135649508-T-C
• rs12466487
• NM_001378107.1:c.1624-394T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378107.1(R3HDM1):​c.1624-394T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,182 control chromosomes in the GnomAD database, including 2,645 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 0.15 (2645 hom., cov: 31)
• Consequence: R3HDM1 NM_001378107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

Genes affected

R3HDM1 (HGNC:9757): (R3H domain containing 1) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
R3HDM1	NM_001378107.1	c.1624-394T>C		intron_variant	Intron 16 of 26	ENST00000683871.1	NP_001365036.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
R3HDM1	ENST00000683871.1	c.1624-394T>C		intron_variant	Intron 16 of 26		NM_001378107.1	ENSP00000506980.1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23534 AN: 152064 Hom.: 2641 Cov.: 31

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.155 AC: 23551 AN: 152182 Hom.: 2645 Cov.: 31 AF XY: 0.160 AC XY: 11932 AN XY: 74414

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.228

Alfa AF: 0.158 Hom.: 494

Bravo AF: 0.157

Asia WGS AF: 0.339 AC: 1178 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.10
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs12466487; hg19: chr2-136407078;