rs698944

Positions:

• chr1-94546355-T-C

Variant summary

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

The XR_007066234.1(LOC124904223):​n.4382T>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 0.901 in 152,250 control chromosomes in the GnomAD database, including 63,381 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 0.90 (63381 hom., cov: 33)
• Consequence: LOC124904223 XR_007066234.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387

Genes affected

LOC124904223 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904223	XR_007066234.1	n.4382T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702722.1	n.155-397T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.902 AC: 137202 AN: 152132 Hom.: 63382 Cov.: 33

Gnomad AFR AF: 0.678

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.988

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.901 AC: 137237 AN: 152250 Hom.: 63381 Cov.: 33 AF XY: 0.903 AC XY: 67232 AN XY: 74434

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.909

Alfa AF: 0.919 Hom.: 14826

Bravo AF: 0.884

Asia WGS AF: 0.962 AC: 3346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs698944; hg19: chr1-95011911;