chr4-144498358-T-C

Position:

• chr4-144498358-T-C

Variant summary

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

The XR_939273.3(LOC105377462):​n.164+63626A>G 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 0.658 in 152,056 control chromosomes in the GnomAD database, including 33,043 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 0.66 (33043 hom., cov: 32)
• Consequence: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377462	XR_939273.3	n.164+63626A>G		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.238+1089A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648340.1	n.138+10883A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99906 AN: 151938 Hom.: 33011 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.658 AC: 99981 AN: 152056 Hom.: 33043 Cov.: 32 AF XY: 0.658 AC XY: 48872 AN XY: 74292

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.641

Alfa AF: 0.672 Hom.: 46451

Bravo AF: 0.645

Asia WGS AF: 0.583 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.14
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7684769; hg19: chr4-145419510;