5-64763160-A-T

Position:

• chr5-64763160-A-T

Variant summary

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

The NM_173829.4(SREK1IP1):​c.13+5345T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 152,238 control chromosomes in the GnomAD database, including 1,104 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 0.067 (1104 hom., cov: 32)
• Consequence: SREK1IP1 NM_173829.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

SREK1IP1 (HGNC:26716): (SREK1 interacting protein 1) Predicted to enable nucleic acid binding activity and zinc ion binding activity. Predicted to be involved in RNA splicing and mRNA processing. [provided by Alliance of Genome Resources, Apr 2022]

LOC124900985 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SREK1IP1	NM_173829.4	c.13+5345T>A		intron_variant		ENST00000513458.9
LOC124900985	XR_007058787.1	n.1689+1815T>A		intron_variant, non_coding_transcript_variant
LOC124900985	XR_007058786.1	n.1689+1815T>A		intron_variant, non_coding_transcript_variant
LOC124900985	XR_007058788.1	n.1689+1815T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SREK1IP1	ENST00000513458.9	c.13+5345T>A		intron_variant		1	NM_173829.4	P1
SREK1IP1	ENST00000495198.6	n.115+5345T>A		intron_variant, non_coding_transcript_variant		3
SREK1IP1	ENST00000506252.1	n.222+1885T>A		intron_variant, non_coding_transcript_variant		3
SREK1IP1	ENST00000510616.5	n.200+1885T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10106 AN: 152120 Hom.: 1098 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0224

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000544

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0667 AC: 10150 AN: 152238 Hom.: 1104 Cov.: 32 AF XY: 0.0650 AC XY: 4836 AN XY: 74456

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0223

Gnomad4 ASJ AF: 0.00836

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000828

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000544

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.00227 Hom.: 2

Bravo AF: 0.0754

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
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: rs6880859; hg19: chr5-64058987;