chr4-153673726-T-C

Position:

• chr4-153673726-T-C

Variant summary

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

The NR_134873.1(LOC100419170):​n.356-4776T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,616 control chromosomes in the GnomAD database, including 3,853 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 0.21 (3853 hom., cov: 31)
• Consequence: LOC100419170 NR_134873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.57

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100419170	NR_134873.1	n.356-4776T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000602666.1	n.356-4776T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31366 AN: 151506 Hom.: 3846 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.207 AC: 31389 AN: 151616 Hom.: 3853 Cov.: 31 AF XY: 0.203 AC XY: 15036 AN XY: 74106

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0902

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.200

Alfa AF: 0.175 Hom.: 518

Bravo AF: 0.217

Asia WGS AF: 0.243 AC: 843 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4696187; hg19: chr4-154594878;