rs4822724

Variant names:

• chr22-26484590-T-C
• rs4822724
• NM_001013694.3:c.209+491T>C

Variant summary

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

The NM_001013694.3(SRRD):​c.209+491T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,036 control chromosomes in the GnomAD database, including 15,643 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 0.45 (15643 hom., cov: 32)
• Consequence: SRRD NM_001013694.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 9 publications found

Genes affected

SRRD (HGNC:33910): (SRR1 domain containing) Predicted to be involved in microtubule-based process; regulation of circadian rhythm; and regulation of heme biosynthetic process. Predicted to be active in cytoplasm and nucleus. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013694.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRRD	NM_001013694.3	MANE Select	c.209+491T>C		intron	N/A	NP_001013716.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRRD	ENST00000215917.11	TSL:1 MANE Select	c.209+491T>C		intron	N/A	ENSP00000215917.6

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67767 AN: 151918 Hom.: 15645 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.446 AC: 67775 AN: 152036 Hom.: 15643 Cov.: 32 AF XY: 0.450 AC XY: 33437 AN XY: 74324

African (AFR) AF: 0.334 AC: 13844 AN: 41456

American (AMR) AF: 0.460 AC: 7024 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1944 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2485 AN: 5172

South Asian (SAS) AF: 0.385 AC: 1855 AN: 4818

European-Finnish (FIN) AF: 0.593 AC: 6264 AN: 10562

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32822 AN: 67970

Other (OTH) AF: 0.468 AC: 988 AN: 2110

Alfa AF: 0.461 Hom.: 6313

Bravo AF: 0.430

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.74
PhyloP100		-0.55
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: rs4822724; hg19: chr22-26880556;