rs698944

Variant names:

• chr1-94546355-T-C
• rs698944
• XR_007066234.1:n.4382T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LOC124904223 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702722.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288736	ENST00000702722.2		n.155-397T>C		intron	N/A
	ENSG00000288736	ENST00000837291.1		n.295-397T>C		intron	N/A
	ENSG00000288736	ENST00000837292.1		n.916-397T>C		intron	N/A

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

African (AFR) AF: 0.677 AC: 28068 AN: 41472

American (AMR) AF: 0.926 AC: 14176 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3461 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5128 AN: 5188

South Asian (SAS) AF: 0.988 AC: 4773 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10620 AN: 10624

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67893 AN: 68042

Other (OTH) AF: 0.909 AC: 1922 AN: 2114

Alfa AF: 0.913 Hom.: 14991

Bravo AF: 0.884

Asia WGS AF: 0.962 AC: 3346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs698944; hg19: chr1-95011911;