10-58756575-C-T

Position:

• chr10-58756575-C-T

Variant summary

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

The NM_001080512.3(BICC1):​c.308-28426C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,036 control chromosomes in the GnomAD database, including 12,718 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 0.40 (12718 hom., cov: 30)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

Genes affected

BICC1 (HGNC:19351): (BicC family RNA binding protein 1) This gene encodes an RNA-binding protein that is active in regulating gene expression by modulating protein translation during embryonic development. Mouse studies identified the corresponding protein to be under strict control during cell differentiation and to be a maternally provided gene product. [provided by RefSeq, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.308-28426C>T		intron_variant		ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8	c.308-28426C>T		intron_variant		1	NM_001080512.3	ENSP00000362993	P1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59691 AN: 150930 Hom.: 12709 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.395 AC: 59713 AN: 151036 Hom.: 12718 Cov.: 30 AF XY: 0.398 AC XY: 29345 AN XY: 73720

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.418

Alfa AF: 0.446 Hom.: 15744

Bravo AF: 0.400

Asia WGS AF: 0.468 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.49

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: rs11815410; hg19: chr10-60516335;