5-66156903-A-ATTACTT

Variant names:

• chr5-66156903-A-ATTACTT
• rs1610942
• ENST00000612404.4:c.*832_*833insTACTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000612404.4(SREK1):​c.*832_*833insTACTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 983,342 control chromosomes in the GnomAD database, including 28,774 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.31 (8759 hom., cov: 0)
  • Exomes 𝑓: 0.21 (20015 hom.)
• Consequence: SREK1 ENST00000612404.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 2 publications found

Genes affected

SREK1 (HGNC:17882): (splicing regulatory glutamic acid and lysine rich protein 1) This gene encodes a member of a family of serine/arginine-rich (SR) splicing proteins containing RNA recognition motif (RRM) domains. The encoded protein interacts with other SR proteins to modulate splice site selection. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SREK1	NM_001077199.3	c.296-2315_296-2314insTACTTT		intron_variant	Intron 2 of 11	ENST00000334121.11	NP_001070667.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SREK1	ENST00000334121.11	c.296-2315_296-2314insTACTTT		intron_variant	Intron 2 of 11	2	NM_001077199.3	ENSP00000334538.6

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47650 AN: 151468 Hom.: 8719 Cov.: 0

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.211 AC: 175699 AN: 831756 Hom.: 20015 Cov.: 30 AF XY: 0.211 AC XY: 81030 AN XY: 384132

African (AFR) AF: 0.543 AC: 8544 AN: 15736

American (AMR) AF: 0.364 AC: 357 AN: 980

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1803 AN: 5140

East Asian (EAS) AF: 0.476 AC: 1724 AN: 3622

South Asian (SAS) AF: 0.205 AC: 3369 AN: 16430

European-Finnish (FIN) AF: 0.178 AC: 49 AN: 276

Middle Eastern (MID) AF: 0.252 AC: 407 AN: 1618

European-Non Finnish (NFE) AF: 0.201 AC: 152955 AN: 760710

Other (OTH) AF: 0.238 AC: 6491 AN: 27244

GnomAD4 genome AF: 0.315 AC: 47748 AN: 151586 Hom.: 8759 Cov.: 0 AF XY: 0.313 AC XY: 23183 AN XY: 74044

African (AFR) AF: 0.502 AC: 20667 AN: 41192

American (AMR) AF: 0.359 AC: 5465 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1178 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2335 AN: 5120

South Asian (SAS) AF: 0.197 AC: 950 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2010 AN: 10548

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14212 AN: 67896

Other (OTH) AF: 0.305 AC: 642 AN: 2102

Alfa AF: 0.101 Hom.: 121

Asia WGS AF: 0.291 AC: 1006 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1610942; hg19: chr5-65452731;