7-76245153-T-C

Variant names:

• chr7-76245153-T-C
• rs7797781
• NM_001110199.3:c.234-3035T>C

Variant summary

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

The NM_001110199.3(SRRM3):​c.234-3035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,220 control chromosomes in the GnomAD database, including 4,490 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 0.23 (4490 hom., cov: 33)
• Consequence: SRRM3 NM_001110199.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 3 publications found

Genes affected

SRRM3 (HGNC:26729): (serine/arginine repetitive matrix 3) Predicted to enable mRNA binding activity. [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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001110199.3. 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
	SRRM3	NM_001110199.3	MANE Select	c.234-3035T>C		intron	N/A	NP_001103669.1	A0A087WXA3
	SRRM3	NM_001291831.2		c.234-3035T>C		intron	N/A	NP_001278760.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRRM3	ENST00000611745.2	TSL:5 MANE Select	c.234-3035T>C		intron	N/A	ENSP00000480851.1	A0A087WXA3
	SRRM3	ENST00000479294.2	TSL:2	n.319-3035T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35537 AN: 152102 Hom.: 4487 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.234 AC: 35561 AN: 152220 Hom.: 4490 Cov.: 33 AF XY: 0.238 AC XY: 17735 AN XY: 74412

African (AFR) AF: 0.205 AC: 8538 AN: 41552

American (AMR) AF: 0.249 AC: 3808 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2325 AN: 5172

South Asian (SAS) AF: 0.196 AC: 945 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3464 AN: 10590

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15219 AN: 68010

Other (OTH) AF: 0.220 AC: 465 AN: 2114

Alfa AF: 0.225 Hom.: 577

Bravo AF: 0.232

Asia WGS AF: 0.324 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	14
DANN	Benign	0.93
PhyloP100		-0.066
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: rs7797781; hg19: chr7-75874471;