15-90954900-T-C

Variant names:

• chr15-90954900-T-C
• rs2001216
• ENST00000555737.5:n.17T>C

Variant summary

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

The ENST00000555737.5(RCCD1):​n.17T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,074 control chromosomes in the GnomAD database, including 6,888 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 0.29 (6885 hom., cov: 33)
  • Exomes 𝑓: 0.29 (3 hom.)
• Consequence: RCCD1 ENST00000555737.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 11 publications found

Genes affected

RCCD1 (HGNC:30457): (RCC1 domain containing 1) Predicted to be involved in chromatin organization. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RCCD1-AS1 (HGNC:54811): (RCCD1 and UNC45A antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCCD1	NM_001017919.2	c.-172T>C		5_prime_UTR_variant	Exon 1 of 8	ENST00000394258.7	NP_001017919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCCD1	ENST00000394258.7	c.-172T>C		5_prime_UTR_variant	Exon 1 of 8	1	NM_001017919.2	ENSP00000377801.2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44620 AN: 151864 Hom.: 6867 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.289 AC: 26 AN: 90 Hom.: 3 Cov.: 0 AF XY: 0.300 AC XY: 21 AN XY: 70

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.289 AC: 22 AN: 76

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.294 AC: 44678 AN: 151984 Hom.: 6885 Cov.: 33 AF XY: 0.298 AC XY: 22108 AN XY: 74312

African (AFR) AF: 0.323 AC: 13395 AN: 41476

American (AMR) AF: 0.346 AC: 5288 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3464

East Asian (EAS) AF: 0.556 AC: 2846 AN: 5118

South Asian (SAS) AF: 0.238 AC: 1149 AN: 4824

European-Finnish (FIN) AF: 0.284 AC: 3008 AN: 10576

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17476 AN: 67928

Other (OTH) AF: 0.299 AC: 630 AN: 2110

Alfa AF: 0.185 Hom.: 625

Bravo AF: 0.305

Asia WGS AF: 0.422 AC: 1463 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.17
DANN	Benign	0.35
PhyloP100		-2.2
PromoterAI		-0.056	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2001216; hg19: chr15-91498130;