3-104543865-G-T

Position:

• chr3-104543865-G-T

Variant summary

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

The XR_007096271.1(LOC105374021):​n.283+5748C>A 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 0.983 in 152,310 control chromosomes in the GnomAD database, including 73,634 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 0.98 (73634 hom., cov: 32)
• Consequence: LOC105374021 XR_007096271.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

Genes affected

LOC105374021 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374021	XR_007096271.1	n.283+5748C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.983 AC: 149607 AN: 152192 Hom.: 73579 Cov.: 32

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.984

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

GnomAD4 genome AF: 0.983 AC: 149717 AN: 152310 Hom.: 73634 Cov.: 32 AF XY: 0.982 AC XY: 73093 AN XY: 74470

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.991

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.979

Alfa AF: 0.988 Hom.: 3432

Bravo AF: 0.985

Asia WGS AF: 0.883 AC: 3069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2961177; hg19: chr3-104262709;