rs7664025

Variant names:

• chr4-90774768-T-C
• rs7664025
• NM_001145065.2:c.2011-40994T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001145065.2(CCSER1):​c.2011-40994T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,858 control chromosomes in the GnomAD database, including 34,429 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 0.67 (34429 hom., cov: 31)
• Consequence: CCSER1 NM_001145065.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 3 publications found

Genes affected

CCSER1 (HGNC:29349): (coiled-coil serine rich protein 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCSER1	NM_001145065.2	c.2011-40994T>C		intron_variant	Intron 7 of 10	ENST00000509176.6	NP_001138537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCSER1	ENST00000509176.6	c.2011-40994T>C		intron_variant	Intron 7 of 10	1	NM_001145065.2	ENSP00000425040.1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101785 AN: 151740 Hom.: 34381 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.671 AC: 101886 AN: 151858 Hom.: 34429 Cov.: 31 AF XY: 0.667 AC XY: 49488 AN XY: 74190

African (AFR) AF: 0.744 AC: 30839 AN: 41442

American (AMR) AF: 0.584 AC: 8905 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3468

East Asian (EAS) AF: 0.678 AC: 3482 AN: 5138

South Asian (SAS) AF: 0.653 AC: 3148 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6408 AN: 10544

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 45076 AN: 67886

Other (OTH) AF: 0.637 AC: 1344 AN: 2110

Alfa AF: 0.655 Hom.: 6450

Bravo AF: 0.673

Asia WGS AF: 0.689 AC: 2388 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	8.3
DANN	Benign	0.75
PhyloP100		0.43
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: rs7664025; hg19: chr4-91695919;